Nah, there were several Christian cathedrals that were converted to mosques by the Arabs long before the Crusades. The Ummayad mosque of Damascus is the most famous example (the Arabs demolished the Christian cathedral), but that was also the case in several Syrian cities, like Homs and Hama. Greek-Orthodox churches also existed in the Ottoman Empire, but that is not a proof that churches were not converted to mosques. The opposite is also true. In modern Greece, there are a few mosques still operating, but the vast majority of them was converted to churches and had their minarets demolished. There were also quite a few massacres, in Crete and also in Asia Minor, especially in Cilicia.

Anyway, it's not a very important point for the enjoyment of the mod. The mistake about the Nisaean horses and Armenia is less controversial and easier to fix.