Many chemical imbalances in the brain are treated chemically. Couldn't this avenue be investigated here?
For all I know, it probably is being. But pumping the body full of chemicals isn't necessarily any less dangerous than invasive surgery. Chemicals inevitably have side-effects, as anyone who has known someone with schizophrenia for a long time will know. And from what I understand, it's about the structure of the brain, in particular the hyperthalamus. There is evidence from the dissection of the brains of a few transexuals who have died (you can't do it when they're living! People need their brains!) that the structure of a transexual hyperthalamus is female, but their bodies for one reason or another are male; or vice-versa in the case of female-male transexuals.
God doesn't make mistakes.
So that means that anyone with any kind of birth defect must be responsible for it, and it must have occured as a result of - what? - sin? So Siamese twins (one of the more spectacular) must have sinned in the womb or something. This is the kind of arguement you're leading to, because if, as the evidence seems to be indicating, transexualism is a birth defect of some kind, then certainly, by this reasoning, someone must have sinned. Maybe their mother? Or maybe all Siamese twins should remain conjoined, because to seperate them would be to disrupt God's purposes for these people?
This kind of theology is the kind that blames the disability on the disabled. There are millions of people with various other disorders of either a genetic or birth-defect kind. Are these people to blame for their disorders, or to leave them without treatment because we're disturbing what God has supposedly ordained for them? Or is it only people with gender defects that are supposed to not want to be helped? Is there something about gender identity that is different from, say, being born with lungs that don't work properly (cystic fibrosis) or with a disease that means that the nerve connections slowly get switched off, turning you into someone who can't walk or talk? Because I don't understand the difference.
And I don't think that God controls everything in nature. God leads and directs the world, but on a day-to-day basis, the universe pretty much runs itself. Otherwise, there would be no free will.
And I'm afraid that there is no evidence whatsever that homosexuality (another but totally seperate naturally occuring phenomenon) is any more prevalent among transexuals than in the rest of the population.
Is it judgement to know something is wrong in your heart and to continue to disagree with the sin while trying to remain friends?
I'm sure you act in a perfectly loving and kind way to these friends. I hope they will remain your friends. But maybe you should do some research into exactly what transgender and other sexual identity issues (such as Intersex and hermaphroditism) actually are, rather than merely jumping to conclusions from a limited and uncontextualised reading of the Bible. Try looking up medical articles on the issue, and don't confine yourself to those that agree with your point of view. Because that way you'll only confirm your ignorance, rather than advance your knowledge. Read all sides on the debate. And talk to your friends about exactly what it is like to feel all your life that you're in the wrong body. Ask yourself what you would feel like to wake up every morning wishing you were someone else, with a different body, from the moment you first became aware of yourself to the present.
I know someone who is transexual (she's a member of our Quaker meeting) and I can see how much happier and complete she is since she had the operation. It's a blessing to know her.