SpecWar personnel are classified down to every breath they take, and vetted in the hardest possible way for loyalty. So if one of theirs was killed and replaced with a tranny, and they were ordered to silence by their CO, yeah, I think they'd still follow orders.
Of course, their own government deciding to slaughter them and then repackage their lives as transexuals might just be a bit of a psychological stretch, even for them. Starting with making think about who's next, and leading to them wondering what the hell they are loyal to anymore. So a bit of an effort would have to be made on the morale side. But that doesn't mean the military wouldn't try such a thing - "assets" are to do with as bureaucrats please, after all.
But then again, if you pull out all of the stops, there's no limits to what can be imagined. Once you throw out Occam's Razor, how do you differentiate between possibility and paranoia?
Otherwise, you have to fold into your accounting that he did 20 years in SEAL team 6, for 13 deployments, including seven in combat zones. That's fairly difficult to cover up. Not impossible, but not easy, either.
I am sure you know far more about all of this stuff than I do.
It bothers and saddens me that I have become such a cynic.