I don't quite understand Inanna's, and I can't help but assume that my earlier arguements themselves don't hold much water...it's always good to throw more variety into the opposition anyway, right? Anyway...
Really, the pursuit of transgendered transition is a pursuit of one's own happiness and peace. Though they go through hell and back, it is the choice of the transgender individual that they desire to cross the perceived fence of gender. I do not think that someone should be called against their wishes no matter how self-scarring because it is their own life to which they deal with the consequences of. Likewise people who take up violent sports, dangerous jobs, and so on are never called off from their occupation and choices over the level of certain damage and present risk that occurs with the said jobs. Please understand that I am refering to the calling that ultimately lies behind it, and it should be valid to permit any kind of calling one's soul yearns for unless if it is destructive towards others.
If there are problems with the calling, then the problems are the primitive and/or minimal supports.
Just my two cents.
(edit: added)
I would like to also remark that it's wary to make practicality arguments. The base argument is hypothetical in the first place. XD It's easily possible that a drug product that can percisely alter the portion of brain can have a significant chance of disturbing other parts of the brain, or even body. Furthermore this kind of drug might turn out to be expensive. (either from resources or more likely complexity of design) As earlier said, as well, if research effectively works at this, people would be wiling to use that medical breakthrough as an inertia in their wishes to produce sexuality-based 'fixes' of a similar design... just...really, a mental altering drug is more dangerous being successful than a failure. :\