First, why did the Dunyain lie to their antecedants about sorcery when they surely knew it was around and not a lie?
1) If there are any Cants to detect Marks on a long-range distance, using sorcery is a dangerous thing for a cult, trying to hide from the world gone mad. Risk of detection can outweight the powers of the sorcery.
2) Using Plato's "Republic" as a hint, before his quest Kellhus was not of the pragmas (philosophers-kings), but of the guardians of the good city. I bet they had a pragma of Gnosis, skulking somewhere in the Thousand Thousand Halls.
3) Dunyain could be quite right in discarding the sorcery. They wanted to hack reality with a nice and elegant move, but not to mutilate it, producing insane amount of T.D.T.C.B. Who knows, may be they even had sorcerer followers before First Apocalypse and found sorcery totally irrelevant and useless for their purpose?
4) Dunyain are people even with their nurtured skills of governing their nature. They simply forgot. Even if they had sorcerers in their refuging crowd, they had no proper school to pursue it's reproduction or population
large enough to have a steady supply of the
Few to reproduce skills from lonely master to lonely pupil. Remember, how Akka taught Kellhus thing dunyain didn't happen to use because of their peculiar lifestyle? Also, two thousand years ago they were... much more human-like, for they hadn't fully elaborated their ideas. That why they could make a mistake here.
5) Deus ex machina. Let it be Cet'Ingira and cants of compulsion, for I love them so badly. Yep, simple is that. Cunuroi, who opened the Arc, now cultivates a human garden, growing a twisted social culture in Ishual. Or, maybe, he's making people to shut it again, who knows. He's a insane erratic after all.