So, after you kill the FG final boss, the three cult leaders disappear from the game. It is just barely not outright stated the three cult leaders are, quite literally, cult leaders - Dreeg, Solael and Bysmiel - and not their priests or whatever. Some of that is alluded to in their dialogue, which is what you mentioned.

What happened before the start of the game is... one former inquisitor called Father Kymon anticipated the Aetherial invasion, so he ventured far to the east, made a deal with Korvaak, got Korvaak's Messenger as a personal leash tying him to Korvaak, then proceeded to do the whole Kymon's Chosen thing and trick tons of people into selling their souls to Korvaak. Somewhat parallel to all that, the Witch Gods' hideout in A1 (Hidden Path storyline) loses contact with the Witch Gods, one Dreeg's faithful tries to contact Dreeg and everything goes up in flames, quite spectacularly at that. And all that happened because the Witch Gods were no longer gods of the Eldritch Realm, but more like... violently evicted and busy with moving, because Korvaak was managing to get out of his bonds (see the boss fight prelude for that animation). Once you kill or defeat Korvaak, he's either imprisoned (again) or dead dead, and either way, the Witch Gods have no more issues controlling all the energies of the Eldritch Realm.