A lot of times it's not even like it's brainwashing. It's like the old soul was plucked out of the body and a new, "better" one was jammed in. There's usually nary a trace of the original person left but we're supposed to be fine with it because the previous personality was an asshole while the new one wants to be better or decent (or at least is willing to be decent out of the self-interest of not dying)
Brainwashing usually implies that the original person is still there, just forcibly changed. This is like the original person simply ceases to exist as the price for our protagonist soul getting to live that life.
At this point we're just debating theology and the existence of a soul rather than if the story is well written or not. Some may disagree.
As I'm no priest I won't weigh in on a side however the point I'm trying to make regardless of dogma, is that isekai authors almost always handle these topics clumsily.
I'll preemptively answer Ship of Theseus-style rebuttals; I suggest that a person's consciousness is nothing more than a collection of memories and experiences. Just as debilitating diseases like dementia or amnesia rob us of our loved ones before they pass on, so do isekai bodyjackers. It's akin to body horror being framed in a positive light.