Emma is evil. She takes pleasure in causing pain, anguish, and manipulating people. Fitting for a serial rapist. She was just crafty enough and picked the winning side. There is no moral ambiguity there. She doesn't believe in what Xavier believes in. She thinks mutants are superior to humans, but unlike Magneto she's willing to wait on inheriting the Earth. It's why she's always spewing out that elitist crap. She's a disgusting waste of a person and Marvel needs to quit pretending she's a good guy.
There is a complexity surrounding Emma that I think Whedon did a fairly decent job exploiting.