I didn't have that problem during the quest. I focused on eliminating the skeletons first before turning on the dragon. My memory is fuzzy but I think one of the skeletons was a magic user. Kill all of them first and see if stops the respawn.
Did that, he was the last to die, but still respawns. Maybe I should take an axe to him to make sure he is dead, I was using a Flame Atronach to kill him.