Our saga has a pious magus and an infernalist. They fully expect to have an epic battle at the climax of our saga, and the players themselves revel in it.
There's no ill will towards each other. It's all about the story.
Until that time, our infernalist is devising very clever methods of remaining "the HIDDEN threat."
That sounds like it will be really fun! Best of luck to you. I think my troupe would find a reason to not like the infernalist because they know out of character, and kill him.
Hence the need for another troupe or to remove the problem players.
This was a different game, but a good game...
I had a character that was heartless, political, and Machiavellian to the extreme. He would twist his friends and lover's and use them as pawns in his schemes. He loses all respect and status in the eyes of his fellows after a major political move goes sour. Broken and near destitute he concocts a scheme to get his old lover back into his life. It backfire's and the last of his "friends" pull away from him forever.
During the entire story arch he has had a protege (another PC) that has acted as a conscience, warning him of every heartless thing he is about to do. My character keeps trying to wear away at the humanity of the protege, while the protege is trying to inspire humanity in my character.
Realizing his life has been ruined by his inability to trust another person. Injured, with no means to travel, he decides to, for the first time in his life, trust another human being, his protege... who kills him as vengeance for something that happened in the past. Apparently the protege had been waiting for many many years for a chance to kill my character. Was awesome.
Neat storytwist.
There's your problem. You play with "meta-gamers."
Meta-gamers are gamers who use out of character knowledge to alter outcomes in game.
We had a problem with a meta-gamer, as he seemed to think of RPGs as something you "won," and saw all other PCs as "opponents" even if he didn't "kill them and take their stuff."
He's the only person in our gaming group who has had no experience as a GM. We all decided to start taking a firm stance with him. Thus, we started denying him on taking meta-game actions, and explain that he is meta-gaming.
He didn't really stop until I started taking away confidence points for meta-game actions. Harsh, I know, but we had to get him to stop somehow.
Just about all groups have their odd "annoying gamer," but it seems like you got landed with a batch of them. Finding a good group is a tentative process, and sometimes requires a bit of luck.
My own group is lucky enough to have been friends for 14 years...two of us for 20. That helps a bit.
I think your SG should have a word with the other players and point out that in Ars Magica, co-operation is a vital element of the game setting. Hermetic magi would have nothing without it: no Parma Magica, Hermetic Magic or Order of Hermes (some might debate the merits of this, but that's another argument). Of course there should be friction between player characters, but certainly not all the time. Perhaps not even very much of the time, depending on individual tastes. However, if the other people in your troupe like playing paranoid, aggressive backstabbers who end up killing each other all the time and your SG seems content to let them get away with it, I suggest giving Ars Magica a bit of a rest and trying Paranoia.
One suggestion for handling metagamers, SG holds all the character data, player gets to know that he´s good at this or ok at that but never gets to see the numbers.
Not perfect(far from it even) but it often helps, because then they lose half the ability to "play by the numbers"(the other half being that they know the rules) and are pushed towards concentrating on "being" the character instead of playing the character.
Taking away Conf pts i think was a very reasonable thing to do.
Could also try penalising XP gains due to metagaming.
On the other hand, meta-gaming can be good too. For example, in our saga everyone knows the story flaws of the other characters. So occasionally our characters do things that we as players know will interact with another character's story flaws and so involve them in the story.
Or if the players know that one character is an infernalist, then we would meta-game this fact. The players know that there is eventually going to be a story about the potential discovery and the succesful hiding (or not) of this fact, and so help to arrange things so that this happens.
I've been in a few games where everyone was 'out for number one'...
They didn't last...
Our current long term game is close to eighty years in... We started in Spring, and have certainly moved into at least late summer. All the Magi have their own agendas, but all know that the others are there to help...
IE We have one tough nut who is about seventy years past Gauntlet. The new Mercere (twenty years out?), just saved his hide when he got jumped. He didn't like it that the new guy saved him, but I would bet a Queen that anyone that messed with the Mercere, would have a WHOLE PACK of trouble coming at him 
When starting your games, try to figure in everyones interests. Try to make sure that everyone isn't competing for the same things...