Beth should still have removed the "essential" flags from camp bosses though.
This, so much this. Why aren't you given one liner radiant quests like the other factions have,'kill camp leader at [random camp]'? Why are they essential at all ? Because of the 'join the Stormcloaks/Legion' quest and nothing more. Try ruining that quest anyway with setessential off, and even if you could, bit late when the war quest-line is over. Terrible, terrible facet of the game.