But it's still not murder. Mordred (had he died) would have been killed by others. His actions were deliberate but his intentions were good.
Obviously this Thing Unsaid is not done and dusted, since in all the legends, Arthur knew what Merlin was and used him accordingly.
Although it was a great scene, I wonder why Arthur didn't pick up on how distressed Merlin was. That was the only thing that marred it. If he had just asked him it might have been so different.