If you don't want them to be essential, then do the Main Quest and the Civil War and then they should not be.
Besides, kicking apart Ulfric's Rebellion is much better than just killing him.
Now, as to why they are essential, they are to the Main Quest and the Civil War, not sure if the Civil War is part of this or not. And, their deaths could dramatically effect the story of the Main Quest. Bethesda is not so worried about the player killing these people off, but the game killing these people off.
I have done the main quest and the civil war, and despite that I was told there were Imperial camps left to clean out, when I try I find the commander is always essential

Hopefully thats a bug that will be patched.
I would also like to see essential status cleared when you have completed all quests for other NPC's.