Perhaps what she let happen was allow intervention of the Gods, which Kehllus knew would eventually happen. Just as he conditioned Saubon and Proyas (sorry, have the audiobook, forgive my spelling) so too has Kellhus laid the ground work for godly destruction of Momem. Such, he implying to Esmi that he was false, and the Gods were against him, ensuring the Thousand Temples is remade to reflect something true.