The final cutscene in EC for Republic showed Kephess still alive with the Dread Masters, and he says "Next time I will kill you." implying we'd see him again in a raid. So that was expected.
The whole Onyxia thing and *other* bosses was just terrible, since we killed them.
I know this is a little offtopic, but I also view QoL as story that isn't retconned.