Your main problem is that those cities are not the same culture as you (Western Med) and will riot, even with a full garrison. I tend to exterminate the populace on taking the city (yup, evil, I know). Then make them an allied Oligarchy.
This will keep them under some control, although you will be running on low taxes with about 400/500 households for each city (will take about 140 turns to expand to the next level). If you have further rioting issues, make sure you have a family member in the city that has some amount of governorship skill.
Failing that and they still riot, leave the city with all your troops, wait for it to rebel, rinse and repeat (there will probably be about 6 people left in the city ;) ).
Hope that helps.
Edit: Oh, yes, it is now down to 40%
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