There's an anime series "Gunslinger Girl" which has girls (nearly prepubescent) treated as mind-controlled tools by some not very nice people who are also the Good Guys. I don't like it but I'm impressed by it as a series in that it exposes a lot of the problems of such a setup unflinchingly. The actual plot is less important, the Bad Guys are pure cardboard but the girls will make you weep for them and the worst of it is they would never understand why.

Warning: this is a very bloody series, if you decide to give it a look.