And she wouldn't be the first -- they've had female Time Lords before. They've even had them in this incarnation of the series, in David Tennant's finale. One of whom, if you read background material outside the show, is supposed to be the Doctor's mother.
If they can regenerate into opposite genders, it totally changes the concept of having children (or even falling in love, like with Rose). And, speaking as a math teacher, if switching genders is a possibility, how come it hasn't happened yet in 10 regenerations? It should have been more likely than that, maybe even more likely than being ginger.
What makes the series work is the interaction between The Doctor and his (female) companions, with the underlying sexual tension between them. The Doctor is an archetypical Alpha Male. It just would not work with a female Doctor.