Makes sense to me. I had thought it was another mod causing the problems anyways. Wonder which one it is?
Sky, there was a question posed on the TESNexus thread that probably should be answered:
"Will this break the DB quest where matteiu bellamont kills the other two speakers in the crypt of the night mother? Or any other faction quest that involves treachery?"
I'd venture a guess that as long as it's done by AI packages, the quests won't be affected at all, unless there's a couple seconds of fighting ( I haven't done any of the DB quests so I don't know). But then I thought about other modded faction quests with that last question. I suppose this would affect them if AI packages aren't used?
I don′t even know what quest is in question, I still haven′t played the game enough I guess.

Anyways, once again this is a simple script that attempts to stop fights that shouldn′t be. And what "shouldn′t be" is based on the one simple rule: if the fighter′s are in the same faction, they shouldn′t fight.
This seems logical and something that should hold across the board, but of course nothing guarantees every quest out there obeys my rule. So no guarantess.

But what it′s worth, IMO it makes no sense if NPCs are forced to attack each other via quest without correcting their standings. If one NPC is an "impostor" and gets caught, and therefore attacked, it would be kinda strange if the same script wouldn′t first remove him from the faction - I mean, wouldn′t the worst case scenario be that some of the members of the faction attack the other members for attacking the "impostor"? A total chaos?
I haven′t fiddled with faction relations myself, but personally I would make sure no such "conflicts" would arise by any chance. :shrug: