IMO Dollhouse was accused of misogyny from the perspective of people who see, in a piece of fiction, literally anything bad happening to a female character as proof of the writer's dislike of women.
Some people have the weirdest ideas of what constitutes misogyny. I guess that they'd also characterize Victor Hugo and Charles Dickens as misanthropes who had an incredible hate for poor people?
And anyway, if they for some reason decided that the series is endorsing what the organization is doing to Echo and other dolls, I don't see what this has to do with women specifically, since there are both female and male "dolls", there's no indication that there isn't an equal number of "dolls" of both sexes, and both male and female dolls are used on sex assignments.
Here's a series of Youtube essays by someone who argues - very well - that Dollhouse is a feminist show, and "some of the most feminist stuff Joss has done". http://www.youtube.com/watch?v=rIcCS6mDEec