As a Social Handicap, it seems like it'd be one of those things where everyone knows he's pagan but no one talks about it out of politeness, but they're still silently judging him for it. Is that what you're going for? 
RoP: Divine, page 70
Social Handicap would work, or a Minor Personality Flaw. Either or.
As for discouragment about what happenned, thw "happened" is still a vague concept so I cannot say.
What did happen?
I'm still working on the stats and writing the backstory, so this is subject to change, but here's the gist of it.
The guy spent a quarter of a century trying to single-handedly stop a crusade. Trying something all-but-impossible, with no help from anyone, getting slowly ground down. Self-imposed labor of Sysiphus. Sacrificed everything for the cause -- bled for it, had his good name dragged through the mud, saw younger magi catch up to him and FAR surpass him in magical power... didn't have time to so much as bind a familiar, let alone train an apprentice... everything he had, he gave to the cause.
Thing is, if he'd succeeded -- if his mundane allies were willing to keep fighting -- it would all have been worth it. But when Saaremaa fell, and his mundane allies surrendered and accepted Christianity, he KNEW he'd failed, and he knew that all of his time, his effort, his sacrifice was for NOTHING. That was the breaking point. The fight was over, and it cannot be picked up again.
Way I see him, when Saaremaa fell, he was despondent. Bitter, angry, furious at the entire universe in general and himself in particular. If the game started in 1227 he'd be completely unplayable. He's had a couple of years to process, so he's not quite as bad off as he was.
For what it's worth, the character concept originally came to me via a section from a Rudyard Kipling poem... that was the theme I was trying to capture.
There you go 
I'd stick with Social Handicap so you can take the Depressed flaw. The latter is a perfect fit for the background you've described.
Also, I don't see Vocis having an issue with Gardaitis's paganism. Vocis's priorities are House Tremere, the Hermetic Order, his family, and his new covenant. He hunted infernalists because they were a threat to the Order, not because they were a threat to the Church. He also spent several years trying to minimize the damage caused by the Albigensian Crusade, so he's seen first-hand that war in God's name is just as base and evil as war in anyone else's name. You can worship the Sky Father or the Maiden of the Grave for all Vocis cares, as long as your worship doesn't put any of his mentioned priorities at risk.
I'm not sure it fits all that well, and here's why. The "Depressed" flaw to me means (in modern terms) clinical depression to the point of being non-functional. Gardaitis is functional. He gets up in the morning, gets dressed, puts his Parma up, etcetera. He may be just "going through the motions" on bad days, but the point is that he still DOES go through the motions. And the stories I want to explore with this character have something to do with him pulling out of the depression.
(Besides, I deal with clinical depression every day in RL. Last thing I want to do is to have it creep into my fantasy life as well. 
)
As far as him being pagan... let's see if I can codify his behavior, and then see which Flaws best represent it.
He is pagan. He does believe in the gods of his ancestors. He does not advertise it, proselytize, or get in people's faces about their religious choices.
He would not attend church under any circumstances, would not follow other religious observances even to 'get along', but would not make a big production out of his refusal either. If the subject of religion comes up in his presence, his most likely reaction would be to grit his teeth, bite his tongue, and keep his mouth tightly shut.
It is possible that something said in his presence would anger him badly enough to make him lose control and say something. However, his anger would have less to do with paganism and Christianity being somehow "right" or "wrong", and more to do with just how much evil and suffering caused by colliding religions he'd seen in his life.
Very Tremere of you
And that is perfectly reasonable.
Just to point out. "modern terms" do not apply to this game. What you describe would be Depressed taken as a Major Personality Flaw, which as you say would result in an unplayable player character. Another point is that Depressed would not be part of your initial V/F package, it would be something acquired latter in life. But, as you wish, this is not something you should do. If anything, a gained personality flaw I would suggest is Oversensitive (to religeous conflict).
It seems to me to fit with a Personality Flaw. And Oversensitive as well. And I don't mind if you have multiple personality flaws.
I have a question regarding a new companion character I'm thinking of. I'm considering giving him Faerie Blood using the Faerie God from Realms of Power: Faerie. Specifically, I'm looking at him having the blood of Hephaistos as given on pg 127 of The Sundered Eagle: The Theban Tribunal. The sympathy I would choose to get the +1 in is Iron. My question is, would that sympathy also cover steel?
I do not have the Faeries book so I cannot be accurate in judgment. But AFAIK, steel is virtually the same as iron as far as magic is concerned.
Same thing here.
We could always split hairs in 4, but this would mean getting into a metallurgy class for everyone, myself included, which headaches as a bonus. I see to recall a discussion between steel and cold iron somewhere...
I'm willing to say iron ≈ steel.
Quick question. I'm going to be making Semyon this weekend. Are we allowed to use the stuff from Apprentices and/or Grogs?
I see no reason why not, so go ahead
I have Grogs, but I do not own Apprentices so I cannot be of much help with that one.
Would an immunity to cold be a Greater or Lesser Immunity? I'm thinking Greater because it is arguably both common and potentially deadly. However, it's less common then the examples given, fire and iron. What thinkest thou?
I think an immunity to weather conditions would be Lesser (and would include rain, sleet, humidity, heat, etc) but an immunity to cold (which includes the whole gamut of Perdo Ignem spells) would be Greater.
I am of two minds on this. The unbiased opinion is that, cold being a subset of weather, Cold would be Lesser and Weather Greater. But if you mean Cold and Ice, meaning immunity to killer frost and being pelded with ice daggers means nothing, then Greater.
I'm thinking, since he's the bastard son of King Frost, that cold, ice, snow, and so on mean nothing him. You could put him on the Wall and he'd be, like, "Pffft. This is all you got? Wusses."
But as far as getting stabbed by an icicle...I'm thinking he would take stabbie damage, but no cold damage.
That would be like saying an Immunity to Fire means that you're not flammable, but the heat still hurts. There's no point in being immune to fire if the heat still causes internal damage, and there's no point in being immune to the chill of ice if the pelting of ice still hurts you. It's like being impervious to metal weapons (as in they can't stab you) but you can still be bludgeoned to death with them.
Though on some sadistic level, I think it would be hilarious if Vibria was in a burning building and died due to smoke inhalation 