When you talk to the guy Imperium wanted killed, and use the dialog options to get him to stop without killing him, you don't get another option when you visit Imperium. I think if you choose the option where you don't kill the guy, you should either NOT get +1 Cruelty, or get another more beneficial intrinsic instead. And of course there should be dialog options where you convince Imperium that the guy has agreed to stop going for the splitup of Imperium (if you chose those options when you talked to the guy).
