Nobody wins, nobody quits, and satisfaction stays out of reach
Mustafa, who had married the daughter of a priest and allowed her to remain Christian, tried to keep Crete within the Ottoman empire by policies designed to encourage Muslim landowners to unite their interests with those of the growing Christian merchant class. But he was swimming against the rising tide of nationalism. The goal of union (énosis) between Crete and Greece had become deeply embedded in Greek national policy and also in the aspirations of Cretans—at least, those Cretans who were both ethnically Greek and religiously Christian. In 1841, despite Mustafa’s liberal policies, another uprising had to be put down in the usual sanguinary manner.
Other Greek Muslims had generally come to consider themselves Turks—as in some other parts of the Ottoman Empire, Turk (Τούρκος in Greek) was used more commonly than Muslim to mean the same thing—and it’s certainly true that, as the century went on and it became more and more obvious that Crete would not belong to the empire forever, increasing numbers of Muslims departed the island for more secure locations. It’s probable that the majority of these expatriates, like the majority of Muslims in Crete, were ethnically Greek. The same Wikipedia article where I found the population chart reported that there are still (or at least were until recently) several small communities of Greek-speaking Muslims living in Turkey and other countries that were then within the Ottoman empire. They wouldn’t necessarily be of purely Greek descent; intermarriage between Greeks and Turks wasn't unusual where there was no religious barrier, and for two centuries Greek had been the language of everyone in Crete who wasn’t speaking or writing in an administrative context (or making small talk in the very highest company).
After suppressing the Cretan rising of 1858, the Ottoman government dismissed the current governor and promised the Christians a few minor measures of self-rule. This promise wasn’t kept, however, largely because it was unpopular with the Crete’s Muslims, who (as was often the case) were very willing to call on Istanbul for defense, but much less willing to comply with imperial policies they disliked.
For ten years or so, the Organic Law existed mainly on paper. Reformers in Istanbul might be willing to grant concessions to the Christians, but the Turks in Crete were much less tolerant, and very little was done.
Independent Greece had not been a combatant, and its delegates had only observer status in Berlin; they weren’t even included in the painting. Their government’s request to have Crete declared a part of Greece got nowhere. But Crete wasn’t ignored altogether. The conference required the sultan to concede genuine political power to the Christian majority on the island, and the result was the Pact of Halépa (Greek Χαλέπα), named for the Chaniá suburb where it was signed, that being where most foreign consulates were located. The agreement not only embodied the terms of the Organic Law, but provided that from now on, Crete would be governed, under Turkish authority, by officials who were Christian.