1) You seem to have missed my point. Re-establishing the Patriarchite greatly slowed Islamification, and the result could be seen a few hundred years down the line. Not re-establishing it does not imply persecution.
2) Islam was an integral part of the Empire? To what extent? Certainly less then most Christian nations of that time. I would suggest the Ottomans attitude towards religion was for more realistic then much of Europe, as opposed to misguided idealistic.
1) I'm quite aware of that. Certainly Islamification was slowed, but it's better than halted at all by constantly raging anti-non-Christian turmoils, at least until the dawn of "Nationalism"....
2) Of course. Ottomans attitude towards religion was far more realistic then much of Europe. That, however, didn't turn the Ottomans away from their Islamic roots. Janissary system, although the primarily purpose of it was for military, Islamization was inevitably included in the agenda as well (despite that Janissary system was illegal according to the Qur'an...).
To what extent, you asked ? Certainly to the point where Islamic principles can't be removed from the Empire by any kinds of reforms....