Good points... My experience with the... weirder bits... of people's religions is somewhat limited. Specifically, it's been a while since I've met a Catholic that took the saints seriously.
Anyway, back on topic...
I notice that cults are a popular topic, and would need to be supported.
It seems to me that Scientology and early renaisance Catholocism could be described by an organization that profits from faith. Since a dwarf would not be able to check the sincerity of another dwarfs beliefs, simply having the god on his worship list should be enough to gain position in the organization.
(I'm going to split religion from faith here. Religion is the organization)
Religion could then be modeled just like any other group or guild, with faith the only membership requirement. Since religious types would judge others at least partially by their adherence to the faith's standards, on average, faithful people should rise in the organization (win elections), however, the deceipt stats (lying, etc) could be used to mitigate those judgements. In fact, since lying is a social skill, and high social skills should be corelated with winning, it's likely that higher-ups WILL be corrupt (or at least, there's a good chance of it).
There's a lot of talk of religion (versus faith) in some of the other threads (including the linked one), so I'll leave that there.
Cults...
What role would a cult play in a fort? How is a cult not a nascient religion?
Could there be something to the refinement process of religions that cuts out the most pernicious beliefs? Would it be better to simply start random religions (1 per 5-10 years?) and just have the 'bad' ones (beliefs at odds with the character of the faithful) vanish quickly? (or get put down).
What tools should the player have to control his dorf's religion? Personally, the idea of a 'bad' cult gaining control of some of your legendaries strikes me as a FUN idea. I know that a lot of players do not like losing absolute control, though. How much ability to repress a dorfs religion is too much?
* By bad cult, I mean cult that encourages anti-social behaviour, whatever that is. Obviously murder, but sex practices could be bad too. Some players wouldn't want ascetics, while others would despise excess children.
It might be a bit much to have suicide cults springing up and converting your legendaries. Perhaps cults (nascent religions) are more likely when dwarves are unhappy?