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?
It certainly could have been a voluntary “demotion” and there is a reason to believe he hasn’t changed a huge amount. There is an issue that needs to be resolved though:
On the one hand, he still seems to have a streak of violence in him the way he slapped Spock (at Spock’s request) in A Private Little War, which would track. On the other, you would think he would have worked with Spock in the plan to get Pike to Talos IV.
If we are to believe the two M’Bengas are the same person, which we have no reason to disbelieve (we can excuse the TOS M’Benga’s lack of an accent), an explanation for why he wasn’t part of Spock’s plan would be an interesting thing to ponder.