True. But if you have a province that is similar in one respect (similar work-sector, similar ethnicity or culture) it makes more sense for it to secede. Imagine Germany conquers France in WW2 and turns it into a province or regiion. That means they handle the problems and uprisings in France as a whole, which makes sense seeing as the French share a common history and culture. And if and when France manages to overthrow the Germans -- either by themselves or with the help of others -- they can become their own Nation again based on the boundaries of that province/region under Germany.
Not exactly "Civil War", but certainly Civ splitting and merging. Provinces/regions lay an important foundation.
And no additional micromanagement is necessary. (Although plenty of ideas about regions DO involve micromanagement.) The system could automatically pick out the French region under Germany, in this case. And satisfying / quelling the French resistance is as simple as building a few buildings (maybe even buildings with regional effects) and positioning more troops within that province, declaring martial law.