Of course intent should be taken into consideration, but even if a writer isn't intending to be bigoted--doesn't mean they can't be passively. That's the really ugly thing with bigotry in general.
You didn't come across as angry, communicating what I'm getting at is kind of tricky right now.
To clarify once again: I am not saying any of this applies to Kill La Kill. I have not seen it.
I'm not even talking necessarily about intent. Intent when it comes to media is largely kind of irrelevant. What you aim to say in a piece and what the observer takes away from it do not always overlap. Though this isn't to say there aren't steps one can take when making media to make your intent much more apparent.
I guess what I'm getting at is that what happens in most popular media is different from actual bigotry. Now, bigotry of all sorts is still a very real problem in society -- but I'm not sure I'm willing to buy that just because a female character in an anime or game is showing skin that it's sexist or contributing to the oppression of women, especially in one that frames it properly with its writing and tone. It's just so... toothless, I guess. I just don't think it's quite the same thing. I'm not even going to say that it's a better or worse phenomenon, just different. And that's even disregarding the fact of the weird hangups people have about sex and nudity, especially in the US.
Representation of women and minorities is a really tricky thing to talk about in general. It's already a complex social issue to begin with, but it only gets even more complicated once you add people's emotional reactions to the mix.
Fake Edit: This is also why I digressed earlier. This post was much longer than I initially intended.
Real Edit: Not happy with this post upon rereading it, added a bit more nuance. Still not happy with it. Oh well.