How about creating additional EVENTS.TXT type entries?
There are already some events in the game which dampen zeal in certain sets of provinces. (Usually involve a scholastic/rational type person or a poem or a popular story is published, which diverts the populace from religious matters). If you can find the entries for these and see how they implement the zeal-dampening effect, then you could control when, where and by how much the reduction occurs.
You needn't search the history books for causes, just cut the description down to "Zeal is in decline across western Europe as <plausible excuse here> gives cause for people to question their faith. -10% zeal in England, France, Germany and Italy".
Unless you want it to happen subtly, without alerts being fed to the player?

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