I personally, would like to have the option to kill anyone. That's just my opinion though. If you take unkillable NPCs out you could possibly ruin the game and quest progressions, however, the reason I personally would be in support of this is because, it would add to the immersion and better serve RP purposes, if they brought back the option to kill anyone.
The solution for not accidentally screwing up something in the game by killing important and quest specific NPCs, is to have a symbol on them that marks them as important, so you'll know, but the option to kill them would still be there, also Beth would have to work out a way to prevent NPCs killing other potentially important NPCs before you even meet them. That's why there are essentials in Skyrim and Oblivion because NPCs would go nuts and kill each other, including ones you needed around.
I just think the option to kill anyone SHOULD be there, just for role play purposes and to improve immersion or realism. Anyone agree? Like I said, the option to kill anyone would work out just fine if there was a way to distinguish between important NPCs and to prevent rogue NPCs killing important quest NPCs.