It was my understanding that any individual who was not living as the sex they were assigned at birth would have to change back before they could be baptized. I am assuming that to change your sex would be considered a disfellowshipping offense. I doubt many people would do that just to get baptized, but you never know.
Personally I think it should be left up to the individual, gender identity disorder is now recognized as a legitimate problem by the medical community. It is not something people choose to do on a whim, or because they are confused or have mental issues. There are various things that happen in the development of a baby that causes gender identity to form, sometimes things go wrong and the child is born with a gender identity that just doesn't match their outside genitalia.
The medical community treats this as a medical condition, and letting the person choose to live as the sex they feel they are seems to work. It's no small undertaking, but it can be done. Treating it as a moral issue, as the Watchtower does, is like blaming a diabetic for taking insulin. They are causing needless suffering to JWs who are born transgender. Imagine losing your family and friends because you have a medical condition and choose to get it resolved, it seems cruel.