Who knows if she was even cured? Can't Mystique block harmful toxins from her body? If she was aware the cure was coming... is it plausible to say that she faked her de-mutantizing? I mean, if that's the case... it makes total sense that she'd be on Magneto's side the whole time.
Another interesting alternate ending that the producers discussed was the ending scene where Rogue and Bobby kissed. After they did so, the camera pans out of the window to reveal Leech sitting beneath it playing a video game or something. Very interesting.