Yeah, most supers don't have the know-how and fine control necessary to do that sort of thing.
But it has come up in comics -- Magneto has done electromagnetic things to brains, various telekinetics have grabbed various internal organs, and I think some electrical hero or villain effectively stunned or dazed someone by messing with their brain. I may be thinking of superhero RPGs on that last one, though.
Well, I'd like to think that's actually where ethics come in.
Magneto did actually use his power to basically paralyze the X-Men by controlling the iron in their body, in one issue, but I can't remember the issue.
A hero might do something like that, but a villain, especially a psychopathic one, would have no qualms about shutting the brain down and using his power to torture.