I'm not saying there shouldn't be repercussions or any negative trait gained, I just think the way it is currently doesn't really make sense. (Also lots of cultures don't really feel obligated to uphold the Geneva Convention, it's only larger more prosperous and globalized nations that strictly adhere to it. And most everyone "bends" the rules a bit.)I would counter and say that the world we live in today has a lot more then 6 culturally different factions yet dozens of these cultures all operate under the Geneva Convention and other such treaties governing how one must conduct war so it isn't outside of reason that only 6 cultures in just a small continental area such as represented with the world map would come together to agree upon a standard governing warfare.
Honestly there is no right or wrong answer here other than what Taleworlds has decided to include as part of their world building process. One part is that in this fictional world, there is a shared concept of honor between cultures and violations of that concept of honor come with certain repercussions. You kind of got to accept that because that is the lore of the game. I mean this is kind of like arguing that in Star War the Sith are actually the good guys because the Jedi had twice before attempted genocide against the Sith Culture. It just doesn't fit the creators narrative that frames the Jedi as representing ultimate good and the Sith as representing ultimate evil.
Let's think about this in the event a character is Honest and Cruel. Like Todd McWarcrimes:
Todd is the feller who always get the job done. Got some cattle you need delivered to a distant city? He'll get them there and he'll make sure any bandits he runs into don't bother anyone again. Are there some peasants complaining about their lands being redistributed? Todd will set them straight by making them an offer they can't refuse. Is there an enemy Lord who just won't stop raiding your farming village? Todd will stop them and he'll stop them for good. Maybe he'll take an eye, maybe he'll take a head. Point is you don't want to be Todd's enemy.