This is something that the creator of each mentioned mod should do.
You're right and to some degree they have. They have done their best not to mess with the vanilla quest lines themselves but I have seen no safeguards in place that protect the MPCs that give out quests. Really it's not one mod thats the problem. It's the the cumulative effect of running them all at once.
The best solution is the kind that has the least impact on the player. I think setting NPC's to essential is intrusive. So setting them as protected seems to be the best solution presented at the moment. As on how to implement that is another question. Modifying the quest that through the CK seems like that only a lot of work but would introduce potential compatibility issues with anything that alters vanilla quests. That leaves us with some sort of fancy script to dramatically alters quests as the player advances in the game. Which could be potentially resource intensive.
Another aspect that hasn't been covered would be to extend a concept that Bethesda has already implemented. A example would be if the shopkeeper was killed a relative would take over the shop in their place. I would say the majority of quests outside of the main quests could actually have the same thing done to them. This approach would take a lot of work but by far with the most immersive if done correctly. In addition there were be no performance penalty and I think maintain compatibility. Someone with more knowledge and experience of how Skyrim quests are created and executed in the game will have to speak on compatibility.