Most (all?) Muslims start with open succession laws making them very vulnerable to hostile takeover. I am not sure what were the historical succession laws, but here's what happens in the game. Christian (or non-Christian, but dynastic takeover from other Muslim rulers at least makes some sense) ruler marries his sister/daughter to some 5th, 6th son of Muslim ruler matrilinearly. No problem, he is so remote from the throne, right? Christian ruler grants his son-in-law some counties/duchies - now he is suddenly first in line and asks him to convert. Few years later middle east is European and Catholic. Who needs Crusades? 
Something feels wrong in this chain of events. At first, it might seem like the problem is due to matrilinear marriage, but even with regular marriage you can get the same situation if the potential heir is invited into European court and granted some lands meaning that he and his children may end up Christian and with European culture anyway. So matrilinear marriage only matters for the human player's gameplay (so that he can continue playing as a blob). But historically it still seems dubious that Christian European character would be accepted as a ruler of Muslim country.
Something feels wrong in this chain of events. At first, it might seem like the problem is due to matrilinear marriage, but even with regular marriage you can get the same situation if the potential heir is invited into European court and granted some lands meaning that he and his children may end up Christian and with European culture anyway. So matrilinear marriage only matters for the human player's gameplay (so that he can continue playing as a blob). But historically it still seems dubious that Christian European character would be accepted as a ruler of Muslim country.