As a note, I think it was common (OOC) knowledge that of the Heirs, generally only the Ardishapur one has any kind of semblance to true faith? Therefore, the acceptance or rejection of Sathol'syn isn't exactly a matter of faith - rather, a matter of law thinly disguised as faith. This might have been different in the old days (a few hundred years ago - that Khanid geezer is old, seriously ancient compared to current Heirs, even if he were, say, a few centuries younger than Heideran was).
So, we can certainly agree that king Khanid II is secular. However, he cannot make his domain secular - since unlike in Europe, the Church is essentially the state in the Empire. Since the Emperor is the head of the Imperial cult - and like pointed out, had been likely for long before Khanid II's time, certainly before his commoners had been born - so the King is the head of his own royal cult in the Kingdom and the head of the Khanid Church there.
Some kind of reformation likely happened to change the key tenets of faith to support the King's rule, with a lot of Scripture that can be emphasized in such of a way that a Royal House can be considered as God's Viceroy/Apostle instead of only the Emperor. The old Apostolic Council and the Emperor's position as being the chosen of the Apostles and/or a first amongst equals of the Apostles might give lots of hooks for this.
Did we have it directly mentioned if the Emperor in the Apostolic period must have been an Apostle himself, or whether the Apostles could appoint someone else outside their number as the Emperor? Because when the Emperor did not have yet complete control of the state, it might have been a bit like the dictator's position in the Roman Republic - chosen to deal with an emergency. (And then the emergency - namely, the Reclaiming of Athra - had been going on for so long that no one remembered a time before the Emperor, so he became a permanent figure.) This is interesting, because we know that the organization of the Apostles did exist at least up to the days of the battle of Vak'Atioth (and may still exist, some of them got murdered in Theodicy, but a lot likely survived). Perhaps Khanid II could find a power-greedy Apostle ready to proclaim Khanid an independent "head of state" of the Amarrians? A bit like old empires on Earth stated they had conquered the entire world, I assume that before the discovery of the Gallente, "the territory of the Empire" and "universe" did mean the same thing for the Amarr. Therefore, the subjects of the Khanid Kingdom are Amarr, but they are ruled by a different ruler. Compare this to West Germany: The Bundesrepublik considered itself the only legitimate successor state in Germany, and therefore, the Germans living in DDR/East Germany were also considered to be citizens.