Now you understand the reticence towards gender reassignment surgery and why someone would be looking for much lower risk pharmaceutical treatments for gender dysphoria, which is exactly what we ended up doing with brain disorders?
It's worth noting that we still do brain surgery on people, and that we're even moving towards using implants to modulate how the brain functions, as opposed to the crude technique of severing parts their brain with rods jammed into their noses or holes drilled into their heads.
I have a feeling that we'll look back on this time when we cut off penises and inverted them into crude vagina like canals, jammed silicon bags full of salt water into chests and pumped people full of hormones as barbaric as the lobotomy era.
They're things that we do out of convenience because they're the best that we have, not because it's what we want to do.
Lobotomies were used as a cure for all kinds of different things. If you knew something was a problem and lobotomy was the only thing that seemed to cure it, is it morally correct to do so as opposed to doing nothing? That's why these simplistic thought experiments are bad because there are examples of what happens when you take it to their logical (and often sadly real) conclusion.