All the scenarios presented thus far are reasonable, but it doesn't change the fact that the Protestant reformation was a direct reaction against the Catholic Church, not the Orthodox Church. The game shouldn't treat these provinces as eligible to receive the effects of the reformation.
I'm not against some unique events that result in the conversion of an Orthodox province to a different branch of Christianity, but those events would be just that, unique, and not part of the reformation.
To me this is also a matter of historical plausibility. EU is of course not about historical events and dates, but it is about maintaining a certain degree of plausibility in the events that happen in game. The reformation can happen in a bunch of different ways, but it's triggering conditions and spreading conditions are still realistic in that nothing truly crazy is happening, like Muslim provinces switching over.