I am noticing that this rumor seems to have exploded in the last few days, and has resulted in numerous edit wars all over the place both here and on places like TV tropes.

My proposal is that until we have evidence to the contrary, we simply go with the official art. The anime in particular is very obvious with showing that Hanji is physically female, with some of the most obvious curves out of the female characters. Her body language is also feminine, suggesting she thinks of herself as a woman.

So how about the simplest explanation, and leave the rest to fan theories or random awesome fandom things?