Louis R wrote:"The Truth will out" became an aphorism for a reason.
Clyntahn was neither the first nor the only inquisitor to sense that something was rotten in the state of Charis. The Charisians were incredibly lucky that he decided to maneuver Paityr Wylsynn into the intendancy -
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Thinking about that, I realised something: Zion defines 'orthodoxy' as keeping the system working the way it is.
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I happen to disagree. What really riled Clyntahn (and most vicars) was the independence of Charis and the dynamic development of political and economic power out of
their control. Royal college or not, innovations or not, the simple fact that Charis was an emerging, independent power was sufficient grounds for his actions. I would see this as part of the ongoing project of the fundamentalist branch of the CoGA of establishing a dictatorial theocracy directed from Zion. (That would help to explain why the Inquisition was able to pull of the Sword of Schueler against Siddarmark; you need to prepare such a major operation over the course of several years). This theocratic drive is what defines Clyntahn's understanding of "orthodoxy".
And the rise of Charis was only partly due to the Brethren; any halfway competent rulership would have led to that rise as population grew and trade picked up after the unification of realms at Howell Bay. Moreover, even Merlin didn't notice any clearly heretical tendencies in Charis when he decided to work from there. His assumption was that Charis was bound to be in conflict with the CoGA in the medium term, and he wanted to use that potential opening. But this whole Hanth business was seen primarily as a power struggle - as it was.
Now, Wylsynn was not Clyntahn's idea; he probably lost a power struggle with Samyl Wylsynn over that appointment, likely because the position didn't matter that much to him and he could use the appointment to his benefit on other matters.
In summary, even without some genuine heresy at the heart of Charis, the CoGA would have moved against them. And thereafter, they would have moved against Corisande, Chisholme, and Siddarmark over the decades, until they had established CoGA rule in all territories.
The reason why this had not happened at the start of the books is twofold:
Firstly, the CoGA was set off on its current course by the reforms of St. Evrayheart and the establishment of the Inquisition as we now it,
secondly, the Out Islands became significant in terms of population and economics only about 200 years ago, I guess.