From my understanding, Crota is some kind multi-dimensional being in that he can co-exist across multiple dimensions at the same time. Little snippet from his grimoire card: "Whispered lore and fragmentary theories suggest that Crota represents a distinct class of Hive entities, not resident in our material world. My latest synthesis of this scattered esoterica suggests that Crota's 'home' is a universe created or remade by his power and occupied by Hive organisms of immense age." So your theory seems correct for the most part. We banished the Crota of our universe but he still existed in his 'home' universe, thus not truly defeating him. We then traveled into Crota's 'home' universe and killed his true form, thus banishing him in all universes that he would exist.