Did the Ottoman millet system really guarantee religious freedom?

Many people have heard that the Ottoman Empire ran a "millet system": Christians, Jews and others each governed their own affairs under their own religious law, with their own leaders. The scholar Abdulaziz Sachedina sees it as an example of pre-modern religious pluralism. The truth is more interesting, and more complicated.

A millet, in the strict sense, was a court of "personal law" under which non-Muslim communities were allowed to rule themselves under their own laws, such as Christian canon law or Jewish halakha. These communities had real power: they set their own laws and collected and distributed their own taxes. All that was required was loyalty to the Empire.

But the "system" part is doubtful. Before the nineteenth century what are now called millets were not at all systematic. Non-Muslims were given a significant degree of autonomy, without an overarching structure. A famous story ties the system to Sultan Mehmed the Conqueror, who after taking Constantinople in 1453 left the Greek Orthodox Church intact and appointed Gennadius Scholarius as patriarch. This was once thought to be the origin of the millet system, but it is now considered a myth, and no such system existed in the fifteenth century.

And "freedom" has limits. Ottoman law regarded non-Muslims as inferior subjects, excluded them from sections of the government and military, and required them to pay extra taxes. The millets had autonomy inside a hierarchy that kept Muslims on top.