See, I look at that in precisely the opposite way...
I just want to win the Civil War but without killing ANYONE on the opposite side.
(Impossible I know)
But your blood-lust is completely misplaced; they are after all your own brothers and sisters.
They are all honorable people and love Skyrim, and just want the best for it.
They simply disagree on what needs to be done and how to proceed...
Why would you desire the complete extirpation of your poor defeated countrymen?
Doesn't make sense.
Well, here's the thing... when the war is over, I typically don't go LOOKING for more enemy soldiers to kill. Problem is, they tend to be hostile when I run into them. Playing as a Stormcloak I stumbled across the Imperial camp in the Reach. I was actually looking for a dragon lair that was somewhere nearby and found them first. As it happened, the dragon I was after came swooping in and began circling over the general area. The Imperial archers started shooting at it.
At that moment I decided that Stormcloak vs. Empire was one thing, but People vs. Dragon was another. I made the decision to come out of hiding and go after the dragon myself. I was actually trying to lure it up a hill away from the camp when an arrow whizzed past my head. It was clearly not aimed at the dragon.
I turned around and found out that the entire Imperial camp was now attacking ME. Me, the person who was willing to put everything else aside and risk her own life to save them from the dragon who they no longer cared about because OMG A STORMCLOAK KILL HER!
After that, wiping out remaining enemy camps didn't bother me so much.
Please note: the fact that I was a Stormcloak being attacked by Imperials is irrelevant, I'm sure it would've been the same had it been a Stormcloak camp and I was playing Imperial. The point remains, I'm not gonna worry about sneaking around all over Skyrim to avoid the remnants of the enemy. Once the war IS over, the remaining soldiers on the losing side need to disarm and GO HOME otherwise they are still enemy combatants. They war is over and they could withdraw, in the case of the Legion, or put down their arms and go home, in the case of the Stormcloaks. But they don't, so they have chosen to remain as guerilla forces operating against the lawful government of Skyrim. Plus, they get hostile when they see me, and I'm not gonna go out of my way to hide from them when they are the trespassers.