Does that mean "if you give a mouse a cookie" doesnt apply to heretics? I guess you could argue the deity is taking a gamble either way: quash and take a loss of followers now, or let it be and hope the heresy doesn't lead to a major loss of followers down the road.
Overall it seems like you treat heresy as primarily an institutional conflict, not one of a crisis in faith on a divine/cosmic level?
So, we need to talk about 'Faith'. Faith is not a preeminent virtue in most religions, and even in modern religions that people may be familiar with - Faith doesn't mean what people think it means. Faith only really matters if works the deity approves of are not sufficient, or if Faith is seen as the necessary precondition to achieving good works. That's not always held to be true. Even where it is held to be true, we modern post-materialism types tend to think of religious faith as 'believing in the existance of the deity', which is generally actually considered to be irrelevant in most theology. 'Faith' in religious terms is generally, 'believing in the goodness, virtue and power of the deity'. Obviously, believing that the deity exists is a necessary pre-condition of the above, but merely believing that the deity exists is not Faith.
Anyway, IMC, there is virtually no one who believes deities don't exist, but alot of people argue about their basic nature - are they good, is there really any difference between the 'good' ones and the 'bad' ones, are they powerful, do they deserve worship, are they actually independent beings or are they merely the spiritual manifestation of peoples collective virtue or vice, and so forth.
For a particular deity desiring worshipers, the goal is to steer as many people as possible into accepting the deities authority over some aspect of their lives. This requires convincing people of the deities basic righteousness concerning that area as well as demonstrating he has effectual power over it. Now the problem is that there probably is only a relatively small number of people whose views about what is 'right' and what is 'wrong' conform entirely to his nature. Now, the deity could reject the worship of anyone that didn't agree with him, and make it perfectly clear in frank and probably threatening terms that such beliefs won't be tolerated, but such actions are likely to convince most potential followers that probably this deity is not for them. (Besides, such actions might be out of character for a God whose basic nature is mercy, tolerance, indulgence, or even laziness.)
So what typically happens is that the deity tries to mollify as many worshipers as possible without creating a schism, or letting the congregants drift so far in their ideology that some rivals ideology might start looking attractive. So deities may have followers who have concieved the deity as having some nature which they find admirable, when in fact he might be uncomfortable with that conception. But what are you going to do, work on altering the conception slowly over time or declare the belief an anathema and start smiting people? Unless you really are the god of vengeful smiting, you probably go for the former most of the time.
Many prominent deities recieve at least casual worship and lip service from followers with radically different views than thier own. Jord (the God of Leisure, Atheletic Pursuits, and basically Fun) for example is probably worshipped by some followers of virtually every alignment. Some have actual congregations and Priesthoods covering a rather wide range of outlooks. It's just not in Jord's nature to come down to hard on people, unless well, they are getting in the way of the fun. Now his wife Sesstra on the other hand...
Extend that to the fact that Sesstra and Jord are often worshipped jointly as husband and wife, and that their priests and priests are often married and sometimes work out of the same temple. Occassional tension in the household is more or less expected. If you don't like that, you end up worshipping Aratos and Aynwen as your idealization of martial bliss.
My only hesitancy is this hardwires into the game world that gods are sustained by faith/belief. I know it's a common trope of D&D at least since Planescape in 2e, but I like leaving it vague whether the gods exist independently of mortals or not. To me it adds to the mystique and power of deities, they can still be creator entities rather than ideological teams with names and jerseys.
I also like leaving the nature of the divine vague. I consider it a campaign level secret whether Zhan was right. And really, even though Kelternists are one of the usual bad guys in my campaign - if you want over the top baby killing crazies they are there for you - I can't say I'm completely unsympathetic with the Kelternists. The 1000 deities of Sartha and how they relate to mortals are patterned largely after the greek gods, and honestly I don't feel that such dieties are terribly worthy of worship either. This is part of the built in tension of the campaign. But you know, you go to Heaven with the deity you have, not the deity you want.