That the Greek Orthodox need special permission to celebrate divine services in any of their churches in what is now Turkey is a dark reminder of Islamic oppression of Eastern Christians from the mid-7th century, and especially from 1453 through the fall of the Ottoman Empire after World War I.
From my article, Ecumenical Patriarch Bartholomew Assassination Plot in Historical Context:
Ever since the Fall of Constantinople to the Muslim armies in 1453, Christians in what is now Turkey have been reduced to second-class citizens (and persecuted nearly to extinction) through the institution of the dhimma, the contract of protection which subjugates Christians to Muslim rule under humiliating, demeaning terms.
Under the dhimma, Christians have to pay the exorbitant jizya tax, cannot build new churches, cannot repair existing ones, cannot share their faith outside their church buildings, cannot convert Muslims, etc. One aspect of the dhimma most terrifying is the concept of "collective punishment." If one Christian violates the dhimma contract, Muslims may attack any or all Christians...
Important to keep in mind is the role played not only by the faithful Patriarch Martyrs, but by other clergy and even monastics in the eventual liberation of Greece... Eventually, the Serbs and Bulgarians threw off the Muslim yoke as well.
It was this series of humiliating defeats during the nineteenth century, and losses in the Balkan Wars of the early twentieth century, which enraged the Turkish Muslims, who turned on the weakest elements of their Christian population, precipitating their infamous genocide against the Christians of Armenia, Greece, Pontus, and Syria, massacring over 3.6 million men, women and children (some dying from starvation, disease and the forced deportations) from 1894 to 1922.
Sporadic persecutions against remaining Christians extended well into the 1950s, perhaps the worst example being the Istanbul Pogroms of 1955, which dealt a crushing blow to the Orthodox Christian community in Turkey.
The Greek population of Turkey had already been reduced to about 120,000 in 1927 (following the main period of the Orthodox Christian Genocide); by 1978 it had collapsed to only 7,000. According to the Human Rights Watch, by 2006 there were only 2500 Greeks in Turkey.
