You forget, Marvel is the company that broke up Peter and MJ because having them apart made for more interesting storytelling, supposedly. Conflict is better, if they're to be believed, and as such, what better than two people who sleep in the same bed being on opposite teams and having to fight each other.
That said, I think the big, fat joke in Norman's face at the end of Dark Reign is that everyone is going to turn on him, regardless of who's behind the door, and kick the everloving shit out of him. So, hopefully, Emma is just doing this to screw with Norm.