If someone feels like he's trapped in a body that differs from the one he wants, I'm enthusiastically in favor of him doing whatever he'd like to do to change his body. He's the one who has to live with it, so he shouldn't hesitate to make any alterations he'd like. But, I just don't buy into the socially constructed elements of gender. I feel that anyone should be free to live any way he wants so long as he doesn't hurt others, and that means throwing all the socially dictated concepts of gender out the window. But, once you've chucked those out the window, what does being a woman or a man even mean, aside from the fundamental biological realities?
For such people, there's no neat fit with either biological category. We really ought to have a third category to accommodate that. But, absent that, for the sake of simplicity, I'm happy to treat them as being in whichever category they'd like. In fact, just for the sake of politeness, I'll treat anybody, intersex or not, as being of whatever category they like. It's not terribly difficult to accommodate, and if it makes them happy, why not? But, I do question why someone else's happiness would, in any way, depend on my definition of gender, or society's in general.
I'd analogize it to the issue around gay marriage. With gay marriage, there's a legal question, and then just a question of terminology. Legally, I believe in equal protection under the law, so I would insist on homosexual couples getting access to the same legally recognized marriages as heterosexual couples. But if someone wants to say that a given legal marriage isn't really a "marriage" as far as he's concerned (e.g., a Catholic who doesn't recognize as properly married a couple where one of the members was previously married and didn't have that marriage annulled by the church), then that's fine, too. It's perfectly acceptable for two different people to have two different ideas of what constitutes a marriage, so long as the law isn't discriminating. And, likewise, if someone wants to say that someone is a man because he has XY chromosomes, regardless of what surgical and chemical alternations he's made, and regardless of how he personally identifies, that's fine. Two people can have two different definitions of gender so long as the law isn't discriminating against anyone.