Like the Revolution of the Netherlands in EU2, you CAN NOT prevent the re-appearing of the pope, since he is too important to the catholic factions (no crusades without him, no forced peace, etc)

But why not let him live in peace in a province of your choice, surrounded by your troops, and THEN you can convert this province to Islam, forcing him to keep a large garrison force. Since the single province only pays fo this garrison, you are safe from him.

If you keep trying to subvert him, he keeps coming back stronger every time (just like EU2).