FYI, I'm working on an NPC faction relations / AIData overhaul mod. This should fix many problems where you see NPCs attacking each other or just bodies lying around. This should also address issues where you enter a dungeon littered with bodies where creatures have attacked bandits.
I think the original solution in Morroblivion was to just increase all the faction relations into the 100s and then correspondingly decrease disposition to player to -100s if it was an evil faction. This design works for the most part if you have a single person party without any companions, but breaks down rather quickly if you want to recreate the complex faction interactions that are present in Morrowind.
Another common issue is where Thieves Guild / Camona Tong NPCs end up dead when they try to steal in public and resist arrest. I'm rebalancing the Responsibility factor so that these NPCs are not so apt to steal and resist arrest.
Also, I'm adjusting the confidence on Commoners and other NPCs which really should not be trying to take on creatures when armored guards are present to handle them.
Let me know if you have any suggestions, issues or comments about these ideas. Thanks.