There are something like 5400 posts which are tagged both "male" and "female". According to the wiki, "female" is for pictures with girls in them, and "male" is for pictures without girls in them. Is the wiki wrong? If not, is there an easier way to clean them up than editing 5400 posts?

Danbooru has stopped using the female tag, but I think we have went against that and still use it. If not, then the female wiki would need to be updated and the tag wiped, but I do believe Gelbooru has chosen to not cease using the female tag.

That's fine, but it doesn't solve the problem of lots of images tagged male that shouldn't be. Something like 10192 does not meet the standard of "overwhelming emphasis on male characters" at all.

About all you can do right now is negate female based tags and and retag stuff right.