More like cleaning up. NG was there when it happened, he had a part in the betrayal and slaughter of the Nonmen of Cil'Aujis.
Cleric indicates that he has spent a lot of time in Cil'Aujis since then. He certainly remembers his way round well enough.
Perhaps he takes them to heart of the topos by habit, or summons Gin'yursis in order to betray the skin eaters and remember, but that doesn't seem right.
Mimara undoes the Topos with a chorae and her judging eye skillz. We know chorae are lethal to ciphrang from TTT (explosive salting). Either her OR the Captain could have pegged their chorae at Cleric and probably banish GY (and killed Cleric).
Based on Cleric's final sermon, I think he is wiping evidence of the Nonmen from history in order to grant their souls oblivion, and I suspect he was colluding with Kellhus to do so.
I have an elaborate nerdanel where, following Mengedda, NG and some of the intact Siqu, Seswatha and elements of the Sohonc used forbidden knowledge from the nonmen mystery cults, the aporos and the quya version of the daimos to enact some term contingency plans including the Dunyain and the Mandate.
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Wracu as pets? Lol!