Unfortunately the Karma system is more like that in the Star Wars (like KotOR: sith or jedi) or Forgotten Realms (like BG: here 2 dimensional) of a global kind of reputation system.
It's not based on local faction reputation of major local factions. Which would mean something like NCR rep, Caesar's Legion rep, BoS rep.
My vision would be a system with:
- a global fame that rises depending how important your action is for the global community but without global moral, moral decisions are part of the faction reps and are based on faction moral or how much you can come close to it
- faction reputations for major factions and each action has different value changes for a faction, each faction has jobs that lower other faction reps and boost their own rep
- once joined a faction or rise in faction rank you get a rep min for that faction that can't be lowered until expelled or degraded, thus joining a faction can restrict you access to other parts even if you take counteractions and only leaving a faction can solve it.
So in order to gain BoS access you must have supported BoS and might not have helped NCR too much or have some higher fame, but to get access to BoS secrets you'll have to be loyal and therefore a low NCR and Caesar's Legion rep no matter how high your fame is. In order to get good BoS rep you would have to think like BoS philosophy and maybe killing a group of innocents to gain tech is good here.
While in NCR killing people for tech would be considered evil. In some factions like the Enclave good is defined what brings back the United States of the old days and evil would be any support of chinese, mutant life or anarchy.
So if you want to be evil or bad karma you just have to join the according faction. And karma level calling like "last hope of humanity" could get replaced by the best faction rep calling like BoS's "saviour of technology" or Enclave's "reviver of the United States" or Caesar's Legion's "visionary of commerce" or ...