The Egyptian cities are the toughest to control, but it can be done without exterminating them. Public order is what you need. You have many ways to keep order: garrison up to 80%, remove culture penalty by destroying Egyptian temples and replacing them with your own (take temples which increase public order and law), but don't knock down the old ones until/unless you can withstand the drop in public order you will get in the short run, Move capitol closer to lower distance penalty, adjust taxes to lower growth rate (zero growth is ideal if the city is already huge), build entertainment buildings and use them as much as needed, keep several spies in each city if you see unrest on the scroll, and last but certainly not least, a governor with high influence and traits which actually do reduce squalor and increase public order will help tremendously.

I've found the governor to be the most potent of all those tools. Seemingly good governors can have nasty squalor and public order penalties buried in their traits. Cheapskate is a killer, and Downright Miserly is really bad, too. Hover over the traits on the governor to see what all the effects are.