Mmkay.. So this is a idea I actually got from another game, but a system like this would prevent a lot of griefing in factions..
So when you join a faction, you have a alignment score, this ranged from -100 to 100, and when you join a faction, you have a neutral alignment, if you kill your own faction members, this gives you a negative alignment with your faction, allowing your own faction members and faction guards attack you on sight, because you are a "murderer" the only way to get back a positive alignment would be to kill enemy faction members.. With a positive alignment, you receive greater benefits from being in a faction, similar to how a faction rank gives you benefit....
This is probably how normal alignment in the game should work..
So when you join a faction, you have a alignment score, this ranged from -100 to 100, and when you join a faction, you have a neutral alignment, if you kill your own faction members, this gives you a negative alignment with your faction, allowing your own faction members and faction guards attack you on sight, because you are a "murderer" the only way to get back a positive alignment would be to kill enemy faction members.. With a positive alignment, you receive greater benefits from being in a faction, similar to how a faction rank gives you benefit....
This is probably how normal alignment in the game should work..