And then the heir converts to his liege's religion later, and I am faced with a having a muslim ruler in France...
a. You say that like it's a bad thing.
It's not like the Fatimids conquered you owing to cheap Muslim shipping and lazy crusade rules. The kid had a bonding experience with her mom's kinfolk and decided France would be better off leaving the tax farm which was the medieval church.
I say roll with it, turn it into an AAR. Better still, load as the kid now and try to grab the Nubian title first. If you need help getting the saved games to work, look here.
b. Your king's already a nutter. What harm can it do?