I think I'm a little late in jumping into this discussion to go through and respond to individual quotes, so I'll my own two cents in here about what I'd feel would be the ideal karma/reputation system. Though I will start off by responding to this:
Karma does not involve human opinion, only reputation does. :shrug:
Agreed. And that's what I originally liked about the old-style Fallout system. Meeting with NPCs and the like, they were really only concerned with what reputations were applicable to them. With that sort of system, I could sneak into town A, steal everything of value, and then "donate" it all to town B. Town A would think I was a horrible person (and rightly so - I'd just nicked all their stuff,) while Town B would regale me as a hero. Reputation is the mechanism by which individual people judge your actions - Karma is the game itself (effectively, the universe) judging you.
Ideally, intent should never play a role in, well, any of this. It's not about what I, or even my character,
think is the right action - Karma is judging you by your actions and their consequences. It doesn't matter if "I'm only stealing from the rich to give to the poor," it's still applying negative karma for stealing (because stealing is wrong) and rewarding you good karma for giving to the poor (because that's a generally nice thing to do.) It's tricky not to spiral this into a real-world discussion of morality, but there are philosophies wherein the same morality applies.
You can essentially break morality down into those actions which are negative to the affected party, and those which are positive (actions thus being either immoral or moral - respectively.) The same rule of removing intention from the action still applies, as we can see. The flawed logic of "I only did this bad thing so that I could do this good thing," is that what you're really doing is accomplishing two separate actions. If you steal from the rich, you're committing an immoral act (because it's negatively affecting the relevant parties.) When you then give those ill-gotten goods to the poor, that's a moral act (because you're positively affecting the relevant parties.) But it's still a separate act. As well, by relativistic standards, the "morality" of the people you're doing these actions to are still separate from the act itself. Stealing items from a "bad person" is still stealing (even if you're then going to give it someone more "deserving.") Also, murdering someone in cold blood (even a "bad person") is still an immoral act. Because you're still negatively affecting that person (obviously.)
A karmic system could very well work in fundamentally the same rules, by that standard. Of course, we'd have to modify things to some degree or another. Obviously, there's going to be lots of killing involved in a game like this. If we made killing anything a "bad karma" action, then everyone would end up skewed towards evil and we'd have an unworkable system. But what I think would be a decent compromise would be to break NPCs down into those who intend to kill you, and those who don't. By that measure, acting in self-defense, while maybe not giving you "good" karma, at least wouldn't give you the karmic penalties of a murderer. And then, pro-actively acting in self-defense would keep you "safe" from karmic repercussions, as well. (So that you could sneak into a Raider-inhabited cave and stealth-kill enemies without worrying about being labelled by the game as "evil.")
There is, of course, the paradox of killing, for example, the evil leader of a very evil faction, even if he's not intending to likewise kill you. Again, I think that can be solved by remembering that the consequences of an action can also be deemed "moral" or "immoral." Let's say we're going to decide to kill the leader of some slavers, even if you have (somehow) a good reputation with them and they have nothing against you, personally. Sneaking into his base and killing him in his sleep might be a "bad karma" action. But you're going to likely regain that lost karma, and then some, by freeing all of those slaves; and likely get a bit of a boost by simply making the world a better and safer place to live in.
Personally, I don't think Karma is the sort of thing where every single thing you do needs to specifically gain or lower each time, either. Killing a supermutant probably shouldn't affect you either way.
And I think the "real" question about Karma is just what role it should play in the game, other than being some sort of metric by which you can judge your roleplaying decisions. (But this post has already gone on long enough, so I'll just let that thought stew for a bit before going down that road all at once.)
And of course, Reputation is, I think, a pretty easy thing to figure out without a whole lot of controversy going into it.