I dont have a problem with the game's Karma system at all. I mean you can complain that you draw your personal line somewhere else and that the whole thing is junk, and that's fine. But at some point they have to pick something and go with it.
The developers have decided to give positive karma for killing an evil person (Legion, slavers) or a hostile violent person (Powder Gangers) or a person suffering in agony (feral ghouls). Lots of people argue that it should be karma neutral to do so or to act in self defense. And yet there are people in the world whose opinion it is that any killing, even in self defense, is wrong (if necessary), and I'm not even talking about pacifists. You might have to kill someone to protect yourself or someone else, but to some people even though that act is necessary, it is still a stain and a moral burden that can never be lost or forgiven.
So there are lot of places you could draw the line on karma and killing. Getting frustrated at the developers for drawing a line of their own choosing in their own video game? Don't bother. There is some justification for it, but it wont work for everyone, so why sweat it?
Even the stealing thing makes sense, especially in a game with factions (societies, cultures). The simple morality of FNV is that stealing is wrong PERIOD ... except for whatever you pry off the body of someone that you were locked into moral combat with. Try to kill me? Your stuff is mine. Otherwise, even though I'm at war with your whole faction, the stuff not on your body belongs to a group, or a person, or a society, or your surviving allies and kin. So taking it is wrong.
You can disagree or agree, but its a good a place as any in a video game to draw a line.
The only place I found, that wasn't really internally consistent with their own philosophy, is Doc Mitchell's house. He apparently doesn't own any of it.

I guess that is a nod to video game necessity. They are giving you a place to loot with no consequences, right up front. I usually don't loot his house, but there you have it.