If the Doctor had become female earlier (by Matt Smith's term at the latest), it would have negated a good portion of the upcoming backlash. Now, there's going to be people wondering, "did they do this based on merit? Or did they do it based on 'superduper radfem diverse inclusive progressive sjw cuck' etc." And as for adapting to female biology, the best possible outcome is that "the Doctor is female now yo, get over it" is the best way to deal with it. Don't make a big fucking deal of it and you have a chance to keep the fans/core audience. Or you know, you could do the total opposite of that and obsess over the fact that SHE will be doing things differently now that SHE is a GIRL and so much better because of it. Because that really sells over good writing and stories, just ask Marvel Comics.