The Thirty Years' War was started in the Holy Roman Empire for largely religious reasons (Peace of Augsburg just didn't cut it for the Calvinist Princes).
In the end, although countries like France eventually joined in for political reasons it was a war that was caused by and deeply rooted in religion.
But then, the princes' decision to adopt unholy protestantism was at least partly dictated by economical and political reasons.
Eh. From my perspective he substantial did damage all of his own. Whatever the case, I think we can agree that religion probably wasn't the cause of the relative decline of the Islamic world.
Hulagu destroyed the very centre of islamic thought, Baghdad, cut of muslim thinkers from patronage in a half of the muslim world, that's why I find him more important.
What I'll say is historiosophy, not history, but I think that what made muslims advance in early abbasid period is that they were feeling, and were, safe and secure. They had a reason to believe the politics point towards their religion as the right one and themselves under God's protection. The byzantine reconquista, the crusades and mongol invasions might have changed that. It may have played a factor.
Especially since one of big myths of the islamic world alive today, but having long roots, is that they owed their success to the purety of faith and to ortopraxy, while saw later failures as results of straying from religious path. There is some true in it, but mostly it's misunderstanding. First because "muslim" armies of VII century were at least partly muslim in name only (not to mention partly christian arab, armenian etc when it comes to land forces, christian coptic and syrian when it comes to fleet, and supported by local non-muslim population), but because muslim culture in the beginnings and at the peak was less religious, less muslim than it is today, at least judging on the lives of umayyad, abbasid caliphs and the lives of arabic poets. Who were, notabene, ruling an empire whose population was mostly not islamic.
But the problem was that while arabic/islamic culture settled and institutionalised, it was becoming less and less open, less tolerant towards other religions, towards allien knowledge (esp. since at some point they were really at the peak), towards sin. One could argue it was doomed to happen that way, but I attribute that also to the trauma of foreign invasion, which was a shock for muslims, who were used to successes. My view is based on an analogy with history of my own nation I guess.
But I believe the main problems were institutionalisation and social internalisation, confesionalisation of islamic faith as well as political trauma of modern political failures as compared to previous success, which caused and still causes people to think that the key to the return to former glory must be found in stricter imposition of islamic law. That doesn't explain why OE didn't spark a new brilliant era for muslim science, though. Perhaps because the flame was already gone.
Mongols' influence shouldn't be exagerrated. Half of islamic world never experienced their conquest, so the damage inflicted there must have been psychical rather than physical.
Again, this doesn't mean islam per se was the reason of Middle Eastern troubles. In early islam, it were the coranic studies that made muslims study arabic language etc.
sorry for a bit chaotic opinion, but I have to go.