So I have finished the rebellion quest in favor of the Stormcloaks, and moved on to pillaging the countryside. I ran across an Imperial encampment (funny how the tides have turned ;p) and decide to continue my war against the Imperial outlanders. I drop all the little minions quick enough, and find that there is an immortal in camp(??).

I drop him to his knees, and then try to decide what to do about it. I decide to loot the camp while I think about the implications of an NPC Imperial that can't be killed after the rebellion quest is complete. I don't want this guy to keep coming after me while I loot, so (here comes the good part), I tell Mjoll to "wait here" right next to the guy, and walk off a ways to watch. He stands up, pulls his sword and Mjoll drops him to his knees in one hit. So I looted the camp while Mjoll watched our immortal prisoner, dropped him to his knees one last time, and ran off.....

I imagine this would work with any immortal NPC as long as your companion can put them down with one or two hits, or uses ranged attacks.

I'll add a question, about the immortal Imperial. Can I go back and re-win Skyrim for the Imperials? What kind of quest related nonsense keeps me from being able to kill this guy?

You can't "re-win" Skyrim for the Imperials. Every camp (imperial or stormcloak) has a invincible leader. I don't know the reason, i only know it's pretty stupid.

Stupid is right. Why why why?

It's especially stupid since your ONE JOB after completing the questline is to find those camps and clear them out. But you can't.

In regards to cleaning up all those camps, I thought I heard the bear dude say as much, which is why it seemed so weird. Anyway, it was cool to find out that companions can play guard duty for you while you gleen what you want from the camp. I'll have to do that more often....