The idea, while "out there," is also a fantastic and unique one, and one that I believe people will connect with once they allow for the possibility.
As far as Dushku's character not having free will or anything of that nature, well... Isn't she, and the other characters, supposed to begin to assert themselves in future episodes? In that fashion, they would start questioning what they were doing, and the "problem" would be somewhat resolved.
That, and, quite frankly, how does lack of free will in this show differ than any movie/show dealing with military forces? Soldiers in combat are essentially the characters from the show; following orders.