So Boerd said
Isn't that exactly when countries have protests? When they have issues?Your source says the religious types were weakened. At the apex of their strength, why didn't they revolt on support of the Caliph in the first Turko-Egyptian war?
And they did - note resistance to French and British rule, respectively.
As for the Ottoman-Egyptian War (starting 1831, unless you mean the Mameluke wars) Muhammed Ali was seen as liberator (from the French) and one who was not defecting from the Empire as such, merely wishing to have greater power WITHIN the Empire, as shown by the fact that Egypt remained a vassal, and he remained the Governor of Egypt. Further, Muhammed Ali did much to modernise Egypt - though shirt-lived due to British intervention - and there was no need to revolt against a good despotic ruler to replace him with a poor one.