I've been thinking a lot about this problem, and I'm glad to see I'm not the only one! My group immediately balked at the coding in this adventure, and I know that they will want something more substantial than the AP has written in. They are in the middle of book 2 right now, and I am already setting up some pieces to lead into what I hope will be a more satisfying reparations arc.
Remember the four faceless stalkers who show up in the lower level of Moonstone Hall? I've decided that they'll be xulgaths who honestly want to leave Sarvel's forces, and will quietly join up with the circus (probably not as performers, just to give them a safe place to be on the surface).
Over the course of book 3, those four will infiltrate the xulgath forces camped around the Swardlands towers, and the group of deserters will grow little by little. At the end of book 4, they will stay with the Empty Stones while the heroes journey into the Darklands. I'm predicting that my players will choose to leave the 6th orb in the vault.
At the conclusion of book 6, I'm planning for Kirosthrek to join the band of deserters as a leader. After Sarvel's threat has been dispatched, the remaining xulgaths will negotiate to set up a settlement near the Welt, where they'll work with the Empty Stones and use their powerful earth-shaping magic to bring life back to the land without the missing aeon orb. Conveniently, one of my players is a cleric of Nocticula, so I just need him to stay alive through the whole AP and they even have a new thematically appropriate demon lord to convert to haha.
Still working through the details, but I'd love to hear what other GMs have done.