It seems a necessary evil to me. At the end of the day a computer game with programmed interactions between the player and npcs can only account for a limited range of events. The world the developers create only makes sense if the players aren't given enough agency to alter the world outside of the conditions the developers have accounted for. Ultimately we can't kill some npcs because the world just cannot react in a sensible way to that death. It's the price we pay for having story, in a sandbox with no story (minecraft) the player can be allowed to do whatever they like but skyrim is a story based game which tries (very cleverly) to weave the illusion of being a sandbox and in order to do so it has to protect the elements of the story.
In many ways the game is like a picture that only makes sense when viewed from a single angle. Move to either side and it all distorts and falls apart. My hope for the next game isn't so much that they make it any bigger than skyrim but that they make it deeper. More routes through quests and interactions, good and evil paths etc.
On a slightly different tack I've realised that even on my most evil of characters I become completely obsessed with keeping all civilians alive. The random vampire attacks added by dawnguard are the worst thing that has happened to skyrim for me and I go to great lengths to mitigate those attacks, even playing a trevor deathhand type. I feel that the npcs are the lifeblood of skyrim and a finite resource. Every one that gets killed diminishes the game slightly (adrianne I'm looking at you here, stop being a bloody hero and run away for once). Besides, where's the fun in being an evil overlord if everyone is dead? What we need is a way to subjugate the population :)