Beside the fact that a humanity system would be unrealistic like nexdemise stated, you pointed out the main problem of such a system: "Every system can be circumvented somehow".
But if you can't trust the system, it doesn't gain you anything; it doesn't give you any additional information because every player you come by might know how to circumvent the system and kill you even if he is flagged as hero/friendly/etc.
In the end it wouldn't change anything.
And like nexdemise pointed out, such a system could mistakenly punish someone for selfdefence.
IMHO another system could help to "replace" the humanity system:
The often requested introduction of beards:
The longer you live, the longer your beard(and/or hair?) grows.
If someone has a long beard, he might be either really lucky or he might be very cautious and KOS. Or he might tend to be friendly but cautious and if you don't approach him he might ignore you.
If someone has no or only a short beard he was recently killed and might be just unlucky or he could tend to deathmatch around the cities and you should shoot first.
You would need to interpret the information, but this system couldn't be circumvented.
I think in the end a (non-ideal) humanity system would give you more of a false sense of security than real security.