Queen Rusudan of Georgia matrilineally married a Seljuk turk (whom converted to Orthodoxy) and their children later inherited the kingdom as Bagrationis, not Seljuks. Clearly it was possible within the Orthodox church, so why is it disabled?
Frequently Asked Questions:
Q: Why can't I matrilineally marry [insert situation]?
A: Both you and the target's liege must have at least Agnatic-Cognatic gender laws to matrilineally marry. If one or both parties are Agnatic it is not possible.