Don't forget two things: 1. We have killed off most of the fallen, not all. We know next to nothing about the house of kings. Their Kell and their servitor are believed to be alive. They are also considered the most dangerous of the fallen houses because we don't know what they are capable of and we know very little about them. 2. The Hive isn't controlled by a single God, their hierarchy is a pantheon of gods, like Olympus. So crota and oryx are only a fraction of their hierarchy