To be clear I do not have a lot of respect for the Emperor's common sense, but I think he would have noticed if the whole population of Cholchis had an intimacy relating to the Thirsting Gods. As for Lorgar managing it in Chaos... he kind of did, he converted them all to Emperor worship, which was indeed upturning the whole basis of their religion. The thing that doomed Lorgar in canon was twofold: the people who kept to the Old Gods were among those closest to him Kor Pheron and company who were able to take advantage of his broken faith in the aftermath of Monarchia and he did not know what Chaos was in canon so he could not look for those hidden cultists who actually did have the touch of the warp about them
As for the example with the Leadership of the Catholic Church... you have just described several quite pervasive medieval heresies and those did not have the leadership of the Church getting behind them and pushing
I'm pretty sure the Emperor did exactly that. He turned up at a Colchis where the population privately worshipped the Chaos Gods and publicly worshipped him, rolled his eyes, and moved on, probably thinking that this was going to be a good excuse to purge Lorgar when his usefulness had come to an end. It wasn't that he didn't recognise it, it's just that he was arrogant enough to see the issue as an opportunity. I think he deliberately permitted the flaws that undermined the Primarchs to set them up to fail. He just thought the failure would be on his terms at a time he'd have control over, not the Chaos Gods, and so he'd win and get the Primarchs and space marine legions to kill each other off, leaving him and what he considered 'pure' humanity the victors. His treatment of Lorgar seems tailored to make him rebel, the Emperor just didn't realise how wide the rot had become or how much the Chaos Gods had arranged for all the bombs he'd allowed to be laid to be set off at once. After all, by then he'd already had the Space Wolves purge two Primarchs and their Legions. I think Lorgar was one of the next on the list.
Just as he was probably planning to purge the Navigators when he's conquered the Webway and do the same to the Mechanicus when he didn't need them.
I think there may have been some people on Colchis who genuinely worshipped the Emperor, but for the most part it was simply a con that the Chaos Gods pulled on Lorgar to make him think he'd won, instructing their worshippers to pretend to defect to him so that he thought he'd won. If even those closest to him could deceive him about their beliefs and remain true to their own faith, why would we assume that the rest of the population who he'd mainly interact with via them wouldn't as well? They're the people who'd be giving him reports and in charge of the education and similar institutions. The people he would have genuinely converted would have been the original Imperial Heralds and the people on the worlds he liberated, who didn't have pre-existing conflicting beliefs.
Famously the Catholic Church didn't deal with persistent gnostic heresies by reeducation programmes. They said 'God shall know His own.' and killed everyone in the general vicinity.
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