One of our troupe members wants to have his companion a failed apprentice. He suggested that the character had experienced a very strong Twilight Episode due to a botch or being exposed to strong magical effects, and the twilight would somehow have "turned his gift upside down". That would mean that the character still has his Gift but he can't use it at all, and it seems to repell other magical effects. That would be magic resitance of some sort.

So, do you think it's appropriate to allow the companion to have a major supernatural virtue that grants him magic resistance of 10 or 15? Or would that be minor virtue (major virtue Guardian Angel grants a magic resistance of 15 among many other powers)

I think it goes against the spirit of 5th Edition rules to give Magic Resistance to a PC, but if you think it works for your Saga, then go for it. Certainly a MR of 10 is no better than what the True Faith Virtue gives, so I see no problem with the power level of what you propose.

I think the reason Magic Resistance is hard to achieve in 5th is to make the formation of the Order, and Parma Magica's role and importance in that formation, logical. If you want to give a PC Magic Resistance and it makes sense for the character, and it's the result of a freak accident instead of some secret tradition of magic that could make Parma obsolete, then I don't see any problem with that. In fact, it's an interesting idea that I may steal for an NPC in my own Saga.

Here's a thought - you could also give the character an Enemy of some over-inquisitive Bonisagus magus who wants to capture him/her for study in the lab to figure out whether the "accidental" Magic Resistance can be reproduced.