Eh, as I said before, Quicksilver is just as defined - if not more - as an Avenger as he is as Magneto's loin droppings. They could just have him and Scarlet Witch as former criminals looking to redeem themselves. That'd be the same as the comics, just without the mutant or Magneto connection. I think they can even use the term "mutant," but I don't know if the term is owned by Fox as well. But yeah, they could still be former terrorists or something, maybe even current terrorists at the start of the movie.
Of course, it'll be interesting to see what they do with him because, frankly speaking, he's not a very interesting character. Then again, I feel that way about the majority of X-Men characters. I find a lot of them very flat, defined by their powers or ethnicity. See: Gambit.