There already is a semi-canon story where the Doctor regenerates as a woman. It's an alternate reality thing, apparently if Time Lords take their own life it causes gender switching (no idea why) and the idea IIRC was that the Doctor took his own life to prevent being found by the Time Lords before he switched into his third incarnation, and then basically went into hiding on Earth.
It's an audiostory called
Exile. Interestingly enough it has David Tennant in it, before he became the Doctor.
