Frankenstein monster is kinda like Trans folks or people

[Sheldon]

No human method can be infallible of course, and the reliability of branches of science vary of course, but this does not mean that they are entirely subjective. Thus science's insistence on keeping an open mind, and that all facts must remain tentative in the light of new evidence, and its ability to admit of an error, and rethink their position in the light of new evidence, is in fact one the methods greatest strengths. 

Knowing something was wrong  or incorrect, still advances knowledge. Clinging to unfalsifiable or demonstrably incorrect doctrine and dogma has the opposite effect. 

Lets remember your claim was that all we had was the subjective opinion of the patient, this clearly is not the case. This is also a complex issue, as we are not just dealing with objective facts, but subjective moral judgments.

If someone were to say "It's wrong for a man to dress like a woman," this is not objectively wrong like a geocentric universe. It's held to be morally wrong, and this is not an objective question. 

Exactly so, moral observations ultimately rely on subjective opinions, so they are separate from objective observations. We can make a moral judgment in the absence of all the objective facts, we likely do this all the time, sadly for some their moral judgments don't have preventing or avoiding unnecessary suffering as an uppermost concern, or at all in some cases, in those judgments.