Some of the Jarls/housecarls are part of quests. If they were killed or disappeared you wouldn't be able to do the quest. Not to mention Ulfric has it out for the Empire not his fellow countrymen.
I'm failing to understand why this is a problem.
Your actions should have an effect on the world around you. If you kill Jarl Balgruuf, then guess what, you can't do any quests that he has. Well, no crap.
Bethesda talked so much of this up leading up to the release, and then scurried like roaches once the "Wait...I thought you said..." questions started pouring in.
Remember how Skyrim was supposed to have an in-depth economy? Remember how we were supposed to be able to affect said economy by our actions? Remember how we were told that we could cripple cities or help them flourish? Then when the game came out and you couldn't do ANY of these things people were all like, WTF? and nobody EVER answered our questions?
Remember how there was supposed to be this big schism in the Mages Guild between the College of Whispers and the Synod? Remember how we ended up getting nothing but a small little sample size of the Synod during the MG quests? What happened to this story line? They made this sound like it was gonna be a huge storyline. And then it fizzled out like a wet fart.
Not to mention that there is no way the Vigilants of Stendarr didn't have a bigger role in the original story.
This game is NOT finished, and anyone who would even attempt to argue to the contrary is lying to themselves. That 11.11.11 deadline was such a monumental sign of marketing ruining a video game that we have ever seen.
This game should have been SOOOO much better, and without the ominous specter of a ridiculously fabricated deadline in place, I think it would have. So many people called this out the second it was announced- Why are you even setting a deadline?
We will wait for you to finish your games Bethesda. Don't even tell us a date next time. Tell us what the game is, and then just make the damn thing, regardless of how long it takes. We don't care, just make it the way YOU want to make it.