Simply converting to Orthodoxy wouldn't work, since his Janissaries and other Muslim soldiers and servants would be very unpleasantly surprised...to have a chance, he'd have to basically ditch the entirety of his old life and reinvent himself as an Orthodox Greek revolutionary. Then climb the ladder to authority and popularity in Greece and get himself elected King at an opportune moment. That's very unlikely from the beginning, but even if he did it - I'm not sure if that man would even "count" as Ali-pasha any more.
If the Ottomans don't stop the breakdown of order and central authority in early 19th century, Ali-pasha could emerge as an independent ruler in Greece...but not a Kingdom nor a Greek state as such. And he'd probably be overthrown. Ali-pasha's religion was only the first among many problems with his subjects, he seems to have been a very cruel and arbitrary ruler as well.