The leadership of the Knights pronounce religious vows, and thus are under obedience to the pope. As a secular quasi-state, perhaps not so much -- which is why I think the pope may either dispense them from their vows or clarify that the vows have no ecclesial significance. The head of the order is treated as a prince-cardinal in liturgical settings; obviously the pope can strip him of that privilege. Moreover, in addition to the Patron (Burke), the Order has a prelate (bishop with ordinary jurisdiction) and clergy under him. The pope can withdraw all of them, and probably will if the order continues to defy him.