Neither is more sensible than the other. The inverse of what you said would be: "To classify it as a physical disorder seems to me to be indicating that the problem lies in how her body is put together, and that her mind is fine the way it is. If it must be classified, it's far more sensible to call it a mental disorder, because you're not insisting that a person's body is somehow wrong." This is exactly as reasonable for exactly the same reasons.
You're operating from the assumption that you can't consider a person's identity to be "wrong" in any way. This is false. A person's identity can very easily be inconsistent with reality in one way or another, via delusion or psychosis or, in this case, something more fundamental. The identity does not match the anatomical reality, and the anatomical reality does not match the identity. Neither is a problem except with regard to the other, and in that regard, they're both problematic.
Except it isn't as reasonable; a body is an object, not a thinking entity. It has no identity to be challenged. If it's wrong, that's simply an empirical condition to be worked around. It carries no necessary moral weight. Changing the definition of a mind
always carries negative moral weight, and so is only acceptable when necessarily coupled with some greater moral good (such as preventing, say, a person with a delusion of wings from leaping off a building while trying to fly, or a serial killer from stabbing people in the face). If there's no need to insist that a mind is wrong, then don't.
I get that they're only wrong because of the disconnect, but since you (as an outside observer) can arbitrarily define either gender as what ought to be (as you've made clear), and the person in question
necessarily has an existing belief as to what ought to be, the conclusion is obviously in favor of the only thinking entity that can put forth a meaningful belief. The actual nature of the body is merely what is, and that's only what ought to be when it isn't hurting anyone.
Yeah, I do ascribe inherent worth to the sanctity minds that I don't to material objects. We might differ on that, and if that's the case then I don't think we're going to get anywhere without a massively long argument about the fundamentals of morality that is far beyond the scope of the thread. I'm not operating on the assumption that a mind
cannot be declared wrong, only that it should not unless all other possible declarations are insensible.