When we first see Dr. M’Benga (chronologically), he is the Enterprise’s chief medical officer. When we see him again, he is still on the Enterprise, but working under Dr. McCoy’s command and, if he was on the ship at the time, under Dr. Piper’s command as well (Dr. Piper was CMO in Where No Man Has Gone Before).
So why do you think he was demoted to a secondary position? Was it something to do with his actions as the Butcher of J’Gal or his killing of Ruh? You would think he wouldn’t be on the Enterprise at all if so. Did Pike demote him? Did Kirk demote him? Was it on orders from Starfleet Command?
What do you think was the reason why McCoy became his superior officer?
Sure, but you could make such points about half the Enterprise crew. They all do a lot of at least questionably legal things.
Think about how many times Kirk violated the Prime Directive and didn’t get in any trouble for it. And on top of that, he literally stole a Federation Starship and, while he did get demoted for it, he still got to be in command of a starship, which isn’t much of a demotion.
Meanwhile, Tom Paris is in a penal colony for being with the Maquis for a few weeks and, as far as we know, never killing anyone, let alone a Klingon ambassador. And then there was Raffi, who got a dishonorable discharge, became a drug addict, and then was readmitted to Starfleet at the rank of commander.
It’s wildly inconsistent.