Like I said, they could believe somebody is going to Hell-- and instead of persecution or anger, the mood can be like a kind of pity for what lies ahead for them-- and of course, chance till the deathbed to repent out of heart, which is in ATL, theology the only way to go to heaven. God is the only one that can judge those going to Hell, and doing God's judgment for him can be considered unholy in itself. .
Your last sentence in some ways captures some of the old Christian view of the Jews - they were dammed, but God would sort them out, and in any event they were needed to play a role in the eventual Apocalypse. Didn't mean that they didn't loathe them any less.
If your truth is the only one, it must be _recognizeably_ the truth. The medieval and early modern viewpoint was that if people reject Christianity, it means that they are being _deliberately_ obtuse, and quite likely are in league with Satan. Heresy is not a difference of opinion, but a revolt against God.
These people are carriers of a lethal spiritual disease which if spread to your friends or children will doom them to eternity in hell. No goddammed way is there not going to be intolerance and at very least some degree of social segregation. Even in the more tolerant eras of Islam, converting from Islam to even "faiths of the book" such as Christianity and Judaism usually meant a death sentence.
The Catholic Church and religious orders led to a lot of scientific discoveries. Even in secular societies, the centers for scientific and philosophical thought were universities, who primary purpose was religious. The Church simply gets a lot of bad press because of the whole "they persecuted heliocentrists" thing. Just make an ATL with a more liberal pope at the time when astronomy and physics takes off, and we will be alright. .
Just a few bad apples in the barrel, right?
(Although Galileo didn't help his case by naming the guy taking the geocentrist position "simplicio")
The church had no trouble with science per se, since God had presumably constructed a lawful universe which could be to some extent be understood. It's when science starts coming up with stuff that blatantly contradicts dogma that the fewments hit the windmill. There was indeed a long tradition of rationalism in the church, e.g. Thomas Aquinas and his reconcilation of philosophy and religion, but ultimately dogma is the bones of an organized religion, and removing some of them is horribly painful. In a theocracy there is nobody to say nay to shutting those pesky scientists THE HELL UP.
As for the WI itself, we can have a TL where there is no protestant reformation, Europe suffers countless devastating wars, and the Papacy forms the basis something like a "Catholic EU" after the world war two analogue in TTL.
While the secular rulers do what, exactly? Secular vs. Clerical power - THAT particular argument was pretty much settled back in the Middle Ages.
Let's step back a minute. How are we defining theocracy? My general understanding was that it's not a true theocracy if the ultimate authority isn't a religious figure or figures: the Caliphate in its early days qualifies, but the Ottoman empire doesn't.
Bruce