I bailed after a few episodes (and then watched some later ones) but my impression was that the dolls were far more victims than anything else. Which is the main reason I bailed - who wants to watch some weepy show about poor widdle victims? I like characters who are powerful and drive the story, not get kicked around and expect us to feel sorry for them.
In a sense Dollhouse was more like "hard" SF than typical TV fare. It wasn't about good vs bad, really, or even about a particular protagonist. It was simply saying, "If this technology existed, how would it affect the world?"
The answer: first for sex, then for violence, and finally as a weapon of mass destruction.