As a general rule of thumb, it’s best not to kill any NPC’s that you know are friendly (such as blacksmith’s and merchants) as they’ll not only cost a LOT of souls to get access to their services again (via a headstone found at the location where you killed them), but it’ll add additional sin to your current total (which is invisible to you).
This sin is then picked up on if you decide to play through New Game + and the Blue Sentinel covenant members will constantly invade you as play through the game (and the more NPC’s you have killed, the more frequent you’ll be invaded).
And the only way to stop the invasions is to die to ‘atone for your sins’. There’s no buying someone off in Dark Souls 2 we’re afraid (so you can knock that idea on the head now).
Regardless, there’s very little to gain from killing them as - apart from their armor set - there’s nothing else you’ll really gain that’s of a massive benefit.
Plus, once you’ve annoyed an NPC by attacking them enough, they’ll not serve you again unless you find a certain NPC (in a certain church tower) who will at least un-aggro them for you (for a cost). And no, paying him off doesn’t work once you’ve actually killed an NPC. So our statement above still stands.