I have an idea it might not completly fix the issue but here it is.
After you have reduced someones health to zero they are knocked out instead of dead and you could have the option of doing a type of Predator style finishing move on them to kill them. Ripping out their spine, dagger to the heart, etc.
If you are Evil or at war with their tribe this would result in positive alignment or tribe faction, and if you are good or neutral and not at war with them this would result in bad alignment or faction.
Then have a system in place that if you are repeatedly knocking them unconcious in a short amount of time attempting to grief them you would lose alignment.
Not perfect I know but it's a start