I think it is likely. Wizards have a long lifespan and Merlin probably does not have a high staff turnover.
It couldn't be any obvious murder. More likely maneuvering his way by sucking up and pointing out others problems. Ya know, how it works in most businesses.
Or fingering others as a traitor. Burning a few fellow spies is a great way to earn trust and sow dissent.In fact, I'd be surprised if several on the Council didn't suspect that's what Harry did when he accused Peabody.