@Gallenger The problem is that we are literally unable to progress the main quest later on due to this.
I did a few quests for the Dozen, then decided I didn't like them and went to the Crucible Knights. Also, I killed off House Doemenel because they were trying to kill me, and because there was a conversation option for that. I usually refrain from killing NPCs because of problems like this, but I figured since there was a conversation option, it couldn't cause too many problems. Boy was I wrong.
Now I cannot get an invite to the animancy hearing from the Crucible, because of my ties to the Dozen; from the Dozen, because of my ties to the Crucible; and from the Doemenels because they ded.
The backup option of getting in with Hadret House is also unavailiable for me. I suspect it is because I would have to ask all three factions for an invite first, which I obviously can't, since I slaughtered the Doemenels...
The worst thing about all this is that I completed the Endless Paths in the meantime. The story content between the last save where I didn't choose a faction yet is rather minimal (~3 hours, very little since I've been binging these last few days), and I'd be ready to redo it, but all that Od Nua progress would be lost...