Though I don't know if this or excommunication is worse, though you should try to avoid either of them.
Bah. While Kinslaying is obviously a horrible crime, excommunication is merely a proud banner of individuality. Usually, if my epic gloriously awesome kwisazt haderach king gets excommunicated, I respond by invading Rome and burn everything in my path...well, I tried but the game's combat system sucks (as in, nonexistent) so I can't actually burn everything in my path, just invade Rome. I consider it pretty historical given the habitual efforts of the Hohenstaufen Emperors to Save the Church From Itself (tm).
But anyway, technically, traits "favor" and "dislike" each other. Meaning a zealous courtier/vassal will have a loyalty penalty to a skeptical lord and and such but will love, I think, a fellow zealot or a chaste lord. "Excommunicated" and "Kinslayer" just happens to be traits that almost every other trait strongly dislikes, translating into a severe loyalty penalty for most characters under you. Except for your fellow excommunicated ones of course. Doomed people stick to each other and prosper.
...whose penalties at least for vassals can be somewhat contained if your character is a brilliant diplomat, prestigious, and hopefully employs an extremely good and loyal chancellor.
Oh, and there are a few bad events tied to those traits. But don't let that bother you.
