Good news then. Forgotten gods is giving you exactly what you seek. There were already some hints about this in base game, but in FG…
[spoiler]… you’ll find out for certain that the witch gods were originally humans. Priestess of Korvaak, some foreign sorcerer and (I think) an “ascendant” - first a mortal man, cursed/ascended by Korvaak to serve as guardian of his main temple (notes I have are not very clear on Dreeg’s history). They seized an opportunity when Korvaak was weak, overpowered him together, and stole his rule of eldritch realm for themselves. Glory to mankind - what could be more glorious than ascending to god?
With such resource as eldritch realm available for the taking, even if you were to somehow clear all the present gods, someone will try to replace them sooner or later. Usually exactly the type of person you DON’T want to have that power. And that’s a big IF, because…
[/spoiler]
Have a talk with him near the ancient grove, or back at his shrine after game restart. We only destroyed one of his manifestations and he acknowledges it as interesting fight, nothing more. If he really perceived player as threat, he could probably just wish us out of existence and go about his business.
Same is probably true for Korvaak. At least Mogdrogen implies that you did not defeat him - you had to have heavy help from the three. The mechanism is not clear, but maybe he can exists in multiple planes of existence and they kept him busy there, or just draining his power in general… If killing a god was as easy as bashing his head, the three could have done it long ago. All they managed was to keep him imprisoned and weakened. Player couldn’t even kill Loghorrean alone when you think about it, just banish him. And that was no god.
As others have said, if existence of gods and inability to just genocide them is your issue with FG, you are looking at wrong game. Void, aether and eldritch realm are going to clash and Cairn will be in the middle of it all. Maybe they’ll annihilate each other in the end, but that is far in the future.