I've noticed that sometimes you gain light point for letting someone live simply because the option to kill him was available, companion affection is also sometimes affected like this. How does this make sense from an RPG perspective? How is deciding not to kill Thana Vesh any different than deciding not to kill every other NPC you meet?

SW:TOR is a good game but a bad MMO, it could be Kotor 3 with co-op and multiplayer and the differences would be minimal. SW:TOR is definitely the better game but that doesn't mean it can't learn anything from pre-NGE SWG.