I don't really think that the surgery makes Ba Reum the good guy at all. Quite the opposite.
See, before the surgery, he was always too good in front of everybody: he would cry watching TV shows, retch seeing a dead cat, and go out of his way to help any and everyone. But now, after the surgery, I feel like his good side is more down to earth: we see him get genuinely confused, and there're longer shots of him by himself, and while he is not (mostly) evil, he's almost plain.
So what I think is: Ba Reum was the real killer all along and he honestly doesn't remember it now. That's why he suddenly understands so much about crimes and the psychopathic mind: because he always knew, but hid it under the pretense of being the best boy. So now, with Yo Han's brain in his head, he's involuntarily using that as an excuse, because he can't believe his own hands had been dirty all along.
Also, I think that's why Han Seo Joon told him he hopes Yo Han's brain doesn't control him: because Yo Han was innocent, and is more entertaining to the Head Hunter to watch Ba Reum being a serial killer and follow on his own footsteps.