Screw it. If you kill a NPC they are dead. There are only a small handful of quests that are required so I just need to protect those NPCs. If you go around killing NPCs then it's less quests for you.
@grumpygamer I love what Dragon’s Dogma 2 does in regards to this. It moves all dead NPCs to a morgue, where they can be revived using a rare-ish consumable. Lets both the player and the world kill them, but doesn’t break the playthrough: just gives the player an extra problem to solve.