The thing is, Wanda is a sub/masochist. She likes to be tortured. (She clearly doesn't like to openly admit it, but she does like it.) Plus as has been mentioned, she's done the same sort of attacking as a merc....

I mean I can see all of the arguments for, and I'm not saying they're entirely invalid.... it just seems like either there's some serious cognitive dissonance going on on the Alliance's part, (entirely possible) or that Stanley has done some pretty awful stuff that we aren't aware of. (Also possible.)