Religious authorities nearly always find a functional role in nationalistic movements, especially in the balkans and the middle east. This is true no matter what the religion.
Some heads of religion - namely the Greek orthodox and the Armenian orthodox played an active part in the planning and execution of numerous revolts during the 18th and 19th century, while enjoying the full protection of the Ottoman state. Other, sunni and shiite leaning bodies did similar deeds working for the Persians or Arabs.
The Muslim sects worked especially hard to bring about a fundamentalist regime in Turkey, during the aftermath of the first world war.
As a result, all independent Muslim religious sects were banned and all leadership of religion was brought under the umbrella of the law at the founding of the republic. As a result, the Christian leadership has been almost inexistent politically, as have the Muslim indepentent sects.
Yet, just like many here in the US still are under the influence of the truths and lies spread about the Turks during the four previous centuries and - as you can see in these posts - fear a return to (quasi) religious rule there, many nationalists in Turkey fear that the intrigue of the Orthodox denominations will return based on centuries of background.
And as you read in even these posts, there are those who openly announce their desire for the partition of Turkey. The result is that the good Patriarch must pay for the sins of others, lambasted by those who cannot know better, due to their own limitations.
I hope you don't think I was "lambasting..."
I know that we in the US tend to see everything through the lens of "religious freedom," not keeping in mind how politics, statecraft, and religion are intertwined.