Nobody wins, nobody quits, and satisfaction stays out of reach
Mustafa Naili Pasha, governor of Crete 1832–1852
Although the Greek mainland became independent in 1832, the great powers, who made all the arrangements, decreed that Crete must continue to be “Egyptian.” Mehmet Ali appointed his local commander, Mustafa Naili Pasha, to govern it, and although he had commanded the army that mercilessly put down the resistance in 1824, he governed Crete in a comparatively mild and tolerant manner for 20 years. For the first 8 years he reported to Mehmet Ali, but the Pasha of Egypt was forced in 1840 to return Crete to the Ottomans. Mustafa, however, continued as governor for another 12 years, now reporting to the sultan. In 1852 he was called to Istanbul, where he subsequently served twice as Grand Vizier. This picture (the only one I could find) was obviously taken late in his life; photography hadn't been invented until then.

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.
Ethnic/religious populations in Crete, 1861
This map was published in 1861, showing Greek areas in blue and Turkish areas in red. (Since the information was probably derived from Ottoman records, the labels are as likely to mean Christian and Muslim as Greek and Turkish.) The large red area in the center comprises the Mesara plain, Crete's richest agricultural region. But of course the two groups weren't as completely separate as the map suggests; it only shows who was in the majority in any given district, as districts were defined by the cartographers. According to a chart I found in a Wikipedia article, the Muslim proportion of the Cretan population decreased steadily through the 19th century. In 1821, the first year of the Greek struggle for independence, it was 47%; in 1832, when independence was finally won, 42%. In 1858, at the time of another Cretan rising, the percentage was 22%, and by 1900 it was down to 11%. Some of this shrinkage is probably due to the reconversion of ethnic Greeks whose families had adopted Islam, or perhaps in some cases pretended to do so while remaining covertly Christian.

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.
Abbot Gavríl about to blow up the Arkadi powder magzine
Christian discontent led to another rising in 1866, the biggest and—in its effect on European popular opinion—the most dramatic since 1770. Turkish and Egyptian troops, brought to the island to suppress the rebellion, besieged the Arkadí monastery, in the mountains south of Réthymno, defended by 259 fighters and sheltering more than 700 refugees, mostly women, children, and old people. According to reports, the besieging force numbered about 15,000, and had brought artillery. The defense was courageous but futile, and when the Turks breached the gates the people inside the monastery blew up the powder magazine, killing most of the refugees rather than let them be captured. (According to legend, the fuse was lit by the abbot Gavríl himself, as in this patriotic painting.) Western Europe got news of this catastrophe immediately, thanks to the telegraph; the first report came from the American consul in Candia. Anti-Turkish sentiment grew strong. Pragmatic foreign policy considerations were stronger, however, and no assistance came to the Cretans from either Europe or the United States (where the issue was briefly debated in the House of Representatives).
Mehmet Emin Âli Pasha, Grand Vizier (for the fifth time) 1867–1871
The Grand Vizier Mehmet Emin Âli Pasha went to Crete in 1867 and set in motion a gradual, low-profile reconquest that wasn’t completed until 1869. The Grand Vizier, a rather forward-thinking reformer, also designed a new policy for Crete, called the Organic Law, that promised Christians a voice in local administration proportional to their numbers. This action, which would have given the Christians a majority, reduced the strength of resistance and helped speed the pacification process. As they advanced, the troops built blockhouses in rural districts so that Ottoman power could be maintained there as well as in the Northern cities where Muslims were mostly concentrated. The Ottoman government feared that, if they let go of Crete, their first line of defense would be at the Dardanelles, just a few miles from Istanbul. World War I was to prove this fear realistic.

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.
Congress of Berlin, 1878
In 1877 a war in the Balkans pitted emergent Christian nationalities, with the active support of Russia, against their Ottoman overlords. The invading Russians were victorious and forced humiliating terms on the sultan, but the other great powers, unwilling to let one of their number upset the balance, demanded an international conference, which was held in Berlin in 1878, to adjust the settlement. A key to the picture identifies the three figures in the right foreground as Gyula Count Andrássy, the Austro-Hungarian Foreign Minister; Prince Otto von Bismarck, the German Chancellor and host of the meeting (officially named the Congress of Berlin); and, shaking hands with Bismarck, Count Pyotr Andreyevich Shuvalov of the Russian delegation. Since Germany had no interests at stake, Bismarck had offered to be an “honest broker” between the concerned parties, all of whose representatives were included in this official painting.

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.