If the player is given a choice of killing an NPC or letting them live (or equivalently, saving them or letting them die), it usually results in the NPC being written out of the story even if they live. There may be a few offhand remarks about them, but you can be almost certain they won't appear in any cutscenes and there definitely won't be any quests centered on them. The reason is twofold. Firstly, as I said above it would take more development resources to maintain multiple storylines (one where the NPC lives and one where they don't, potentially multiplied if an arc involves multiple such NPCs). Secondly, it would cause backlash from players who kill the NPC and later discover they're blocked from doing some side quest where that NPC plays a key role.
It will quickly get difficult to maintain a consistent world and storyline if players are allowed to make impactful choices. I suppose there would be some merit in a system like Star Wars: The Old Republic's light/dark side meter; being able to choose my character's motivations and having a kind of permanent record of them made the choices feel meaningful even though they really didn't affect the story at all. It would be difficult to suddenly add that sort of system in a new expansion though.
