Unfortunately with mods like Skyrim NPC Immersion Mod, Deadly Dragons, Occupy Skyrim, and Wars IV NPC's quest giver's get killed. Therefore truncating quest lines. So I propose a mod that flags some vendors, quest givers, and unique citizen's unkillable or something depending on the situation or the progress of quest.

So when the quest is completed the characters involved in them become non-essential (killable) Of course some special cases need to be made for NPCs who need to be killable for certain quests. It would really be nice to find another way besides flaging NPC's essential but I personally can't think of an elegant solution. What are your thoughts on how the should be implemented and is anyone willing to take the mantle?

This is something that the creator of each mentioned mod should do.

I'm thinking of just protecting vanilla. Although it would be neat to see some sort of tool to scan and protect quests added by mods.. but that's a little far-fetched.

Making NPCs protected - which means that attackers will cease to attack them when they go down to 0 unless they're the only target around - might do the trick.

I disagree; none of the above mentioned mods have anything to do with the default behavior of Bethesda-made quests.

A mod like this would unfortunately be a bit tedious to build, as you're going to have to go quest-by-quest and SetEssential particular NPCs depending on the quest stage. It's possible to do this in such a way as to not cause a conflict with other mods that might modify that quest by simply running a script in the background that does a GetStage on (perhaps many) quests and performs SetEssential operations as necessary. This would be performance-intensive however. The other option is to edit the quest fragments of these quests and add the SetEssential lines as necessary there, but any other mods that edit those fragements would be incompatible. I don't know if other mods (USKP?) made modifications to these fragements for bug-fixing purposes.

I think the idea has merit however and should be investigated.

True, but. Just batch editing most NPCs in towns to be Protected would be faster and less arduous. Also lets the player continue to kill NPCs that they wish to.

Wouldn't it be easier to have a local script forcing NPCs to yield and flee to indoor locations when fighting enemies they can't possibly beat? There is a mod that accomplishes that (Fight or Fly), would be a matter of expanding the conditions to include things like vampire attacks (in Dawnguard), dragons and civil war battles.