I wasn't disagreeing with your conclusion, I was questioning your reasoning.
This is in direct opposition to the definition of Karma. Karma is a religious concept where good things happen to good people and bad things happen to bad people. Good karma players having higher luck and bad karma players having their luck lowered would be a perfectly valid expression of Karma in the game. The problem isn't in the logic it is in the game design, rewarding one style of play and punishing another is too heavy handed, you are pushing the player down a path they might prefer not to go down.
Not trying to be nit picky, just trying to stop the thread veering off at a tangent.
Agreed with this point about the nature of karma.
Some general thoughts regarding that--
In game terms, I think karma should be thought of as good or evil acts with consequences that cut across all faction lines. Racking up bad karma doesn't necessarily have to be all bad, at least short term. Think of the classic short path to power. If you kill people for their stuff, you get their stuff. That's a reward right there. Later on you may get something of a come-uppance. On the opposite side, doing right all the time should be harder. You should struggle more. But, there could be rewards down the road.
Doing things that are karmically bad could even result in intangible rewards. We have precedence in FO3 with the Dreamcrusher perk. Many games essentially have a karma line with rewards on both ends. Generally in these things, doing bad nets you abilities to help hurt others. Going good helps protect yourself or others. Knights of the Old Republic is a good example.
In sum, I don't think treating karma as it is usually understood to be would necessarily force anyone down a path or end up rewarding some choices more in game terms. Plan it well and it could be very balanced while still keeping the idea of good things happen to good people, bad things happen to bad people. Remember too, karma doesn't always pan out in this lifetime.

I'm pretty sure that works by the player essentially becoming a part of the NCR faction. In other words, it would not, in fact, work for stealing stuff from people who are hostile to you.
I'm actually not very far into the game. I only understood the stealing penalty after I cleared the prison of Powder Gangers because they seriously torked me off. That's one reason I haven't dived into this fully. I want to finish the game once to get the big picture and then go back and flip all the right flags.
For becoming allies with a faction and then being able to steal all their stuff, I think assigning ownership to a dummy faction would solve this neatly. However, I'm not sure what other implications that may have and a lot of testing would have to be done in game areas I'm not familiar with.