I like Emma a lot, but I have no idea how she and Scott managed to stay together as long as they did. They just don't come off as compatible, personality-wise. Really, I'd like to see them just sort of be like "This isn't working out" and agree to just be friends. And hey, if somebody wants to bring back Scott/Jean eventually, that'd be great, so long as he gets some space before rushing back into a relationship. However, this being X-Men, that is highly unlikely to happen.
That being said, though, I still doubt Emma's actually evil. She's the sort of character who'd make a really good double agent, and I hope they've gone that route since it would actually be interesting.