The whole karma idea is bugged throughout the game. Roy threatens everyone in Tenpenny and he's a 'good' guy even after murdering all the residents (assuming he's permitted to live)? Sorry. It doesn't make sense any more that the fact you can hunt down slavers and shoot them on sight for good karma.
Lots of pretty fussy decisions who make karma hard to sett. If take the caps and go out and kill him and his gang it's evil as he has not done anything. Negotiating so the ghouls can live in Tenpenny tower sounds good, yes it's go to hell but it was no way for you to know, yes had you heard Roy discuss that he wanted to kill everybody it would change everything.
Same way, enslaving raiders give bad karma, now if I was a raider I would prefer being enslaved than killed. However you might say you support and expand slavery by doing so it's bad.
And you have the cases who is impossible for the game engine to judge, I once tried to save a wastelander from a radscorpion, Long range and the wastelander was very low in health, Tried a sneak shot on the radscorpion in VAT, around 30% chance for hit but hit the wastelander instead, I got negative karma for murder. No way for the game to tell it was a desperate rescue attempt.