1. General comment: it's a good idea to write out the acronyms, at least in the first occassion in which you use them. I wasn't immediately sure what those terms meant. For anyone reading, SRS means soemthing to the effect of "surgical (gender) reassignment," and HRT means something to the effect of "hormone (gender) therapy." He's referring to snipping vs. injecting a gender-confused individual.
2. You are mistaken. There's a number of ways that I could go with this, but here are a couple of thoughts:
A. Even you would have to admit that SRS and HRT are used to treat a healthy patient. If I were to ask you if the patient is sick, you would, perhaps, say "yes" for ideological (as opposed to medical) reasons. If I ask you what the sickness is, I won't accept "he has healthy male organs" or "she has healthy female organs" as an answer. Those aren't diseases.
B. Your answer demonstrates a failure to understand nature (in the Aristotelian sense). Note, I'm not faulting you with this: this is, of course, something which is, at least nowadays, fairly obscure. For Aristotle, nature is an intrinsic principle of motion and rest. Things develop in the way that they develop because of what they are.
Dogs naturally grow with four legs. Why? Because they are dogs.
So here, you'll perhaps tell me that it is unnatural for the patient to have male or female organs.
I'll ask you: are these organs healthy or unhealthy?
You'll have to say "healthy."
Why, then, did the patient develop healthy organs of that gender?
Because the patient is of that gender.
C. Finally, your answer presupposes a Cartesian splitting of mind and body as completely separate, autonomous substances (which you, as an atheist and a materialist, cannot grant). If it be granted that the intellectual soul directly informs the body and makes it what it is, then your answer becomes unintelligible.