How exactly do you do that? Just leave the current system with crouching in place unless you personally kill them with an attack? It would be a programming nightmare, they'd have to make the damage you do to opponents in some way different than the damage opponents do to others, or inflict upon themselves.
Ugh a Bethesda defender. Had to happen sometime. Here's my take:
Keep the system in place where they go down on one knee.
When in that bended knee mode, the player gets a warning about the essential nature of that NPC to a quest.
If the PC still hits them while in bended knee mode, the "essential" is removed when they recover.
This essential flag is only removed IF the player has done damage to the NPC while in bended knee.
Other NPCs are coded to ignore bended knee NPCs (set agro to zero) so they never hit NPCs and remove their essential flag.
That should *not* be hard to code in! I'm not a programmer but given all the other things they code in this game, I don't think this would be akin to solving world hunger. What knowledge do you have that this would be so difficult?
If it IS like solving world hunger for Bethesda's shoddy coders (I'll throw in that they have brilliant art/music/world/lore designers just to show I'm not a hater) then come up with another solution like having essential NPCs in static safe areas or a player toggle in the games menu.
And in ANY event unflag any quest NPCs after the quest is finished for god's sake.
It's dev laziness not to come up with a better solution than having every quest NPC in the game be unkillable. The immersion breaking factor of Maven Black-Briar all up in my face and protected by some immortality code is beyond irritating.