I think it might be interesting to depict the Athar splitting into two factions with the end of the conflict. This might allow the disjunction I found between the various groups of the Athar to be reconciled.
It'd be pretty cool if the Athar became something like this....
Seekers of the Divine
A group of Athar that have found the existing Powers in the Multiverse to be not worthy of worship. The Seekers of the Divine primarily are looking for a purpose and unity to the universe that they can revere. All of the Priests of the Greater Unknown come from this faction but also individuals that revere other cosmic and non-anthromorphized forces (Good, Evil, Death, etc). The Seekers of the Divine are less hostile to existing gods but simply don't view them as worthy of worship.
These would probably make their headquarters on Mount Celestia or openly in the Outlands as the gods no longer really OBJECT to their presence. They'd probably be allied with the Mind's Eye and Fraternity of Order.
The Godless
This is made of the Court of the Godslayers merged with a lot of the people that don't want to join up with the Seekers of the Divine. They'd probably be allied with the Bleak Cabal, Doomguard, and the Sodkillers. The Godless are people who reject all Gods and many actively work to thwart their efforts across the Multiverse. They're genuine atheists as much as people who know that powerful beings who control afterlifes exist can be.
The militant faction of the Godless is inspired by what they've done and mostly attempt to target the worshippers of weakened Gods or screw with other races across the Cosmos. Ur-Priests (From the Book of Vile Darkness) might fall into this place as well. Most members just openly express their disdain for gods.
I think it'd be cool if they gain the Faction Ability to be immune to direct divine retribution (but can still be hunted by servants of deities).
I would be a bit wary of making all atheists into a separate faction, at least officially. Even without the whole Hellbound Asmodeus-feast, it is rather iffy to take a real-life minority and set them, practically unchanged, into a fantasy world and write a story surrounding them without offending numerous people.