What is it that you have in mind?
Gardaitis Kallas was born and raised on the island of Saaremaa, off the coast of Estonia. I'm thinking he was born about 1175 or so. Estonia is technically part of the Novgorod tribunal, but he was discovered and apprenticed by a Rhine tribunal Flambeau. Due to a major issue with his magic (Short-Ranged Magic), as well as his affinity with self-transformation, School of Ramius was the only logical choice for him. Gardaitis was Gauntleted in 1199, and inducted into the Ash Guild. (Quick, look astonished.)
Estonia in general, and Saaremaa in particular, was one of the remaining strongholds of Paganism in Europe. Gardaitis was very strongly pagan -- still is. In 1198, Innocent III declared the Livonian Crusade, and in 1202 the Livonian Brothers of the Sword were formed in Riga. This did not sit particularly well with Gardaitis. (His mundane family might have been caught in one of the Livonians' early atrocities -- I'm not 100% sure yet.)
Gardaitis, full of Ash Guild ideas about how magi shouldn't be afraid of mundanes, attempted to get some of the northern Rhine covenants to do something about the Crusade. Needless to say, he failed dismally. Individual magi may have been willing to help out a little bit -- here and there -- subtly -- but overall moving against the crusaders in any significant way was seen as a Really Bad Idea (tm). The issue didn't even get to Tribunal -- it was made clear to Gardaitis that if he so much as opened his mouth he'd be laughed off the stage.
So, being a young hot-headed Flambeau, he decided to do something about it himself.
For the next several decades, he abused the hell out of the peregrinatores system. He'd guest at one of the northern Rhine covenants (Oculus Septentrionalis, Crintera, Heorot) -- pay his dues in vis or covenant service -- and then essentially use the covenant as a place to store his stuff. He'd come back once in a while for a season or two of study or lab work, but he spent the majority of his time in the field, attempting to single-handedly stop the Livonian Crusade. Spying on the Brothers of the Sword, sabotaging their equipment and supplies, helping Osselians (the inhabitants of Saaremaa -- the island is also called Osel) train and fight, taking the field himself, etcetera. He wasn't above getting his hands dirty with an occasional assassination either.
Quite obviously, this bends the Code into a pretzel. I'm pretty certain he got hauled up on charges of interfering with mundanes at least once. He was, however, subtle and careful, and most of his magic wasn't flashy, so he managed to avoid censure. It's also possible that there are things he did that would get him punished if the Quaesitors ever knew about them -- I'm pretty sure he had something to do with the Bishop of Linkoping's death in 1220, for example.
However, wizard or not, subtle or not, one man trying to hold back a crusade is an exercise in futility. In 1227, the Brothers of the Sword crossed the ice to Saaremaa and took both of the major strongholds... and the island elders surrended, and accepted Christianity.
Gardaitis could not stomach that. That was the end of his personal crusade. He FAILED.
He's in Andorra for one reason at the moment -- it's as far away from Saaremaa as he could get without falling off into the ocean. He's also really not sure what to do with himself. The cause that was the central focus of his life, the cause he lived and breathed every day for 30 years no longer exists... and without it, he's no longer sure who or what he is.
Thoughts? Opinions? Comments? Thrown fish?
I imagine there would have been por-crusader Flambeau magi as well. How would you have delt with them?
And how will you cope in a covenant where most of the covenfolk and several of the magi are Catholic?
Not to discourage you. Just to consider. There is a crusade against the Cathats in Provencal and a Crusade against the Saracens in Iberia. And many of these magi have battled against the Infernal.
Good question. I'm not sure whether he ever ran into any, but his first impulse would probably have been to try for a non-fatal solution. A "gentleman's agreement" to stay out of each other's way, perhaps, or a certamen/duel with the loser agreeing to stay the heck out of the area for a period of time.
Interesting. Apparently, the Code matters more to him than I thought. Or at least the provision against slaying other magi does.
He TELLS himself that it wouldn't matter -- that he's going to face a situation like that pretty much anywhere he goes. I don't know if he's right. Honestly, I don't quite know how he will cope: I'm not deep enough inside the character's head yet. I'll have to figure that out in play.
I don't think it's going to be an insurmountable issue, though. I'm still figuring out his mindset, but as far as I can tell, he's not pagan because he denies the existence of God... he's pagan because that's what his ancestors were. He's certain that Christianity is A valid path to follow. It's just not HIS path... and his anger over the crusaders' insistence that he and his people must not worship in the way they choose is probably what was at the core of his actions.
(Comparing the crusaders to the Founder of his House and his "join or die" policy, and noting the extreme levels of irony, is left as an exercise for the reader.)
Anyway. Christians who are both devout and militant are going to make him twitch, there's no question about it. Thing is, he's probably de-humanized his opponents in the course of his struggle... reduced them to caricatures in his mind. "Oh, they're all alike, they're all X and Y and Z". Those stereotypes aren't going to match the reality, and I'm curious to see what he'll do when he realizes that's the case.
However, if you feel that would be too much trouble to deal with, or won't fit with the overall tone of the game, I can come up with another concept.
Nobody is really a devout militant. I think. One maga flip-flops betweet calling herself Catholic or Jewish. I think a few are Pagans also. I do appreciate diversity, so go for it 
It doesn't become an issue for you unless you choose to take Pagan as a story flaw. Otherwise it is just part of your background.
But it seems a pretty strong part of your background. Where do you want to go with it?
And what does your character believe are the origins of House Flambeau?
How about Guillaume?
Of course, none of this is tied to religion, so no problem.
I assumed he meant devout Catholic militant.
He definitely has the Pagan story flaw. Not quite sure yet where exactly I want to go with it.
In re House Flambeau origins.... Upon re-reading the relevant section of Societates, I can definitely say that he knows more than his player remembered off the top of his head. Feel free to ignore the bit of snark in my previous post. 
Well, Solomon is a former Benedictine monk who believes it is God's Will that he became a magus, and that the Gift is a gift from God. So while he may not be militant, he's definitely devout (ie. Pious major flaw).
Vulcanus isn't particularly devout, but he is Christian, and is quite militant. He has been on Crusade because Christianity is Correct, so taking back the Holy Land and spreading the faith to the heathens is the Right Thing To Do.
Yeeah. I can foresee Vulcanus and Gardaitis having... heated discussions. Hopefully not literally heated.
So it is a mixed bag. The Major Story Flaw implies you are a devout Pagan and adamant about it. You don't have to take the flaw, but if you do it will generate stories.
I recall no snarky comment made.
And the player probably remembers better than the character 
Refer to the House Rules and setting details for this saga. Your character can have varied and diverse thoughts about the Founder, I wanna play with the concepts of Flambeau Apocrypha. But the player will be well served to refer to ToH: Iberia from ArM3.
I am not a fan of intercharacter strife.
Inter-character disagreement and mild conflict is good in my opinion since it tends to lead to fun roleplaying. When everyone's always in agreement it doesn't feel as realistic and fun to me. But I agree that strife should be avoided...
At least in campaigns when that is not expected. I played in a great campaign once with a lot of strife. One friend went through six characters in seven sessions at one point. But we all knew that was the game we were playing in, and we knew we could play it safe too if we really wanted.
Religious debates never seem to work out in Ars Magica like they do in the real world. In Mythic Europe, the Divine is identifiable, observable, and quantifiable... which makes it really difficult to roleplay a pagan, not to mention trivializing the whole concept of faith. (How can you have "True Faith" when you can prove the existence of the Divine? It's not Faith if you KNOW it's real.) It's one of my few real gripes about the AM mythos.
Actually, I'd respectfully disagree. (Disclaimer: this is nothing more than my opinion.)
Magi don't know all THAT much about the Divine. They know that there is some observable and quantifiable Power that is inimical to magic. They know that this Power is strengthened by adherence to rituals of Abrahamic religions. They know that devout adherents of Abrahamic religions can occasionally evoke manifestations of this Power. They know that magic targeted on these manifestations usually fails.
The existence of this Power is not in question. But the mere fact of its existence does not necessarily tell someone very much about this Power's aims, properties, intentions, or true nature. There is a very large gap between acknowledging its existence and believing in all the articles of the Christian/Jewish/Islamic faith... and it is that grey area that both doubt and True Faith call home.
Plus, the existence of the Infernal, the fact that the Infernal is ALSO inimical to magic, and the fact that some magic targeted at Infernal manifestations ALSO mysteriously fails -- all of those serve to enormously complicate matters. The 'advanced knowledge' that magi possess would not, IMO, make it less likely for them to fall int apostasy. Indeed, I think it would make it more likely.
Ryu, I've been thinking about it, and there's a pretty good chance Vulcanus and Gardaitis know each other. They were trained in the same Tribunal, and Flambeau is a tightly-knit house. It's very likely that they met at least a few times, and know each other by sight/name.
Also, if Gardaitis needed a magical item crafted, he'd probably try to order it from a Flambeau who's known for enchanting skill. With your permission, I'd like to go ahead and say that one of his items was crafted by either Ivarr or Vulcanus himself, depending on the timing. This would also make sure that their in-game interaction is more polite than it otherwise would be.
You OK with this?
Hoise Flambeau is not really tightly knit. They form small societates within their house, but these divergent groups may or may not interact with each other. And they don't often order items from each other. You may have connections, such as a Mentor, otherwise you would most likely go through the Mercere or Verdi.
I respect character diversity, but I am not so keen on conflicts. I have an idea that perhaps you should take Pagan as a Minor Personality Flaw (I will grant that option, Fixer thought that one up long ago). It is part of who you are, it defines you, but you need not cause or react in conflict just to stay in character. You are different, you don't talk about it and if need be you endure and just put up with the fact that you are a minority.
This would mean toning down your religeous militant background a bit. Perhaps a different cause? Something that conflicted with your beliefs and caused you to travel elsewhere?
Just ideas.
And just to put it out there...
In setting, Divine monotheism is the higher power, but it is also true that this cannot be definitively proven. It isn't Abrahmic, it is monotheism. Sol Invictus has nothing to do with Abraham, yet still qualifies ad Divine. Theoretically, I would imagine some variations on Hinduism would also be Divine (in that all the various gods are just forms of the aspects of a single divine consciousness).
That'd be fine. As long as Gard never says anything heretical or critical of the Vatican around him, he'd be fine. Vulc is also School of Ramius (seems like all the Valdarians would be) and would probably be a sparring partner or whatnot.
Wow. That's not one I've ever heard before 
I've actually got it down as "Social Handicap (pagan)" at the moment, but a personality flaw might work too. I'll have to think about that.
I'd lean towards making him be even more deeply discouraged by what happened than I originally thought. Would that work, do you think?