I totally agree that karma is really stupid and definitely very badly implemented. But I can see what Bethesda tried to do. The problem here is that you are all considering Karma as a personal thing when it is a universal thing instead.
It doesn't matter if we kill an evil, sadistic, psychopath in self defense (reasoning: because we are defending ourselves it should be neutral), it is still a good act because we removed this person from this world, it will prevent this evil from continuing doing horrible things. If we kill a savage ghoul in self defense, it is again a neutral act, but we are finally ending the suffering that this human being endured for so long (maybe even centuries), this in a universal scale is a good thing (I guess) while in a character's personal scale is a meh. In these examples, your actions are contributing for a better world, and karma is about making the world a better or worst place.
If you steal something, you're becoming a worst person (in theory, each case is a case), so by becoming a worse person, you're making the world a worse place too (I guess).
Also, I can't remember anymore to be honest, but I think that you only lose karma from stealing from any "evil" faction if you're in good terms with them, the exception is that if you steal from NCR or Legion, you always get bad karma, even if they hate you.
Karma in NV is broken- I think even one of the devs said that. They were trying to scrap FO3 karma and make new one, but they hadn't time to implement all parts of the new one, so in some ways NV karma is worse than FO3. For example killing Gangers gives you karma, but picking their guns from the table where they were splitting loot from robbery takes karma.
I also think that FNV was going to totally revamp the karma system but they run out of time. There are things that make no sense in FNV karma and look rushed and not much effort was put into it, while others we can tell got great care to be implemented. I think that it wasn't a "you're good or bad" in your face thing, but it was to be used as a hiden value that would unlock dialogue options and reactions from NPCs (in dialogue too).
But the final verdict from me? I can see what Bethesda tried to do with the Karma system, but it sucks anyway. Not only that, but it was badly implemented too. In FNV it seems like it was gonna be refined, but it ended up mostly a really messy and stupid thing too.