Maybe the buffs and debuffs a religion gives could be tied into the strength of "zeal" the religion enjoys in a community. So a very closed minded socienty with a high Zeal level might get a number of Buffs like "Deus Vult" (better troops against unbelievers), "Inquisition" (higher repression, i.e more socially stable society at the cost of more violent uprisings IF it does revolt) and "Religious Arts". However they would also receive debuffs like "Closed Minded" (lower tech advancement), "Religious intolerance" (higher unrest through different religions present) and "Don't talk to infidels" (worse diplomatic relations with non-Zealos or other believing societies).
If the country had no or little religious Zeal, the debuffs and Buffs received would be near zero.
What debuffs and buffs the religion recieves will be tied to the religious tenants chosen when the religion is "built", an example of such a tenent could be "Smite the unbeliever" wich gives the aformentioned "Deaus Vult" and "Don't talk to infidels" (de)buff
Also fun fact talking about religion: today is Ascension day
I would say those are more symptoms of a low "Zeal" score. If you have a high "Zeal" score, no atheists will be tolerated, if you have a 0 Zeal score, there's no believers in your country (I imagine the "Zeal" score to be a mixture in measuring how big a part of the poplulation is religious and how fanatic they are about it). Also secularism in itslef doesn't mean you can't be religious, it just means you devide the state and the church.
There are some other possibilities like nations with a lot of religions (like India) or syncretic religions (like the roman pantheon) where a zeal score wouldn't make a lot of sense. There's also the possibility that a nation doesn't tolerate religion (i think communist states are suppossed to be that way?).
About communist states, there could be a mechanic modeling how certain political decisions affect the Zeal level in a country. However, simply stating that a country can "ban" religions is simplified. The ex USSR has large portions of very religious populations of different Christian and Muslim faiths, and while China has the most atheists in the world, China also is the country with the biggest Population in the world so thats a kind of Biased statement. Notably, even tho there's huge restrictions placed on missionaries, I think I read somewhere that China also has the biggest growing Christian population in the world (showing that there seem to be many people there that are not only very open to the idea of religion, but open to the idea of a religion that is rather foreign to their country and culture).
HOw to deal with syncretic religions and multi faith countries... I have no Idea. One thing that you could do is include a "Zeal bar" for every religion that has a certain % of the pop as their believers. If there are different religious populations in a country, a high Zeal level on one or more religions could increase religious tensions, kind of whats happening between the Hindu and Muslim/non-caste populations in India at the moment. The buffs and debuffs a country receives due to religions could be scaled with the population, so if 90% of a country belive in Religion A and 10% in Religion B, then A's effects would be multiplied with 0.9 and B's with 0.1 This would lead to interesting strategies, where you could try and make up for some religious debuffs for your majority of pop by having a carefully controlled minor religion to offset the effects with their buffs.
I had a quick thought that I figured would fit decently well here.
Basically, these are researches in the field of social science that the player could implement in the Government Editor:
Both the spiritual and secular government traits (or policies/virtues/whatever) give their government a boost in legitimacy in the eyes of the populace. However, the spiritual traits would tie into the "zeal" mechanics tammio suggested (and thus would fluctuate based on religious fervor), while secular traits, although not particularly strong or weak, would be more predictable, since they're just founded on reason.
To add to this, the two categories could be used against the government; governments that use spiritual traits as a source of legitimacy would have to defer to the divine authority vested in the church (unless you feel like pulling a Henry VIII), or risk losing divine right/the next election, while secular traits leave the government open to be challenged by other means ("Social Darwinism" has that challenge in the form of a coup d'etat, "Social Contract" has it in the form of ideological upheaval over whether the current system serves the people best).
Alright, so that wasn't so quick, but just throwing it out there.
I don't think the religiousness and authoritarianism of a nation should be fixed, because those tend to change quite often, especially with revolutions (like the french and russian ones), but also by more peaceful ways (like Hitler's rise to power).
Besides, it's important to remember that the point of view of the government is not necesarily the same of the people (which might also not be the same for all people).
mitobox I like this Idea, because that way you can have a libertarian but very religious state. As a (not perfect but usable) example of that the USA comes to mind where Christianity, or at least some form of it, has a lot of influence on politics. However I would more express it as an xy coordinate center, with the 0 point being where a society has both 0 faith (meaning its atheist or at least agnostic but simply doesn't care about religion) and 0 on the Liberty vs Authority scale.
So if you follow the x-axis (religious) you will find 2 extremes, either 100% Zeal or -100% Zeal, representing a perfectly fanaticly religious society, or a society composed exclusiveley of militant atheists (thinking "religion is the opiate of the people" but with EVEN MOAR ATHEISM AND VIOLENCE).
On the y-axis would be a scale with Absolute Authority (An allmighty Governement) vs Absolute Anarchy (NO government) on both ends (interestingly then Liberitarian thought would probably be somewhere around y=0 then)
I will draw and upload a graph when I'm home later
PS: Aslo if you want to make this model even more complicated and infeasable we could expand it into 3D by implementing a Z-Axis wich would describe "State control of markets" vs "Free Market". This would mean that perfect comunism would then be found at -100% Religion, +100% State, +100% Authoritarism, while Capitalism would be at 100% Free market, -100% Religion, and I can't really decide if it would be 100% Anarchy or 100% Authority (to create perfect markets you would need 100% authority I think)
This is fun So I'll think ybout one other, Feudal Monarchy: Needs: Devine Right, So 100% Religion, Needs Loads of Power to Nobles, BUT NOT THE KING so 100% authority but a high but not 100% (maybe like 50%?) State Control of economy score to represent the very controlled markets of feudal systems (near 100%) but lacking the centralization (so minus like 40%? = 50 to 60%)