I know one of the promo images did put an X on Emma's uniform, so hopefully that means she is going to be part of the X-Men. I hate when they try to backtrack Emma's character 30 years to turn her into a villain again. If you are going to do that you might as well make Rogue and Gambit villains too since Rogue started out in the brotherhood and Gambit was a member of the Marauders.
Emma is morally grey but she is no where in the league of crazy as Magneto, and would always see Sinister and Apocalypse as enemies. Emma doesn't even have close to the killing body count as Logan, Laura, and Psylocke.