I have completed the quest line for the empire and am now clearing out stormcloak camps anly I have come across a fellow by the name of Arrald Frozen-Heart who is unkillable.

Is there any way for characters who are essential on one quest line to be set to not essential after that quest line is closed?

I can no longer become a stormcloak so no stormcloak quest giver needs to be essential.

for some reason the generals in the camps are always essential. best to avoid them.

Unless bethesda fixes it you have to either use the creation kit (pc) or possibly console commands (also pc)

Aye, I was annoyed by their essential status too. I was playing the opposite was a Stormcloak and wiping out Imperial camps. I could kill everyone but the damn general.

Once you choose a side to join, the generals for the opposite side should lose their essential status.