I always felt if you committed to one side of the conflict, that should immediately take the opposing camp's NPCs off essential status.
Yeah that would have been nice .... along with removing bounties if you kill an opposing faction in your home faction's hold. Why should I get a bounty for killing a travelling group of Imperial soldiers a mile from Windhelm?
Been there, killed some stormcloaks. Walked into Solitude...'Wait a minute...I know you'
Really? I just slew your enemy and you want to throw me into jail?
Guard got Fus Ro Dahd over the wall.