I suspect there will be two types of rebellion; a national rebellion caused by strong Republican or Monarchist sentiment, which will work pretty much like civil wars in MTW; troops will mutiny and/or rebels appear based upon how much revolutionary sentiment there is in each province. You will then have the option to support the rebels or the government, with both sides being essentially the same in terms of units.

The other type I suspect will be regional rebellions like the United Irishmen or the Jacobites, which will be caused by sheer unpopularity of the foreign ruling power. In these I suspect you will not have the option to control the rebels but these rebellions will be more unique and dependent on the region they occur in. Possibly these could even be emergent factions, since from the campaign map shots it's clear CA have no problem with including loads and loads of factions this time.

Well, that's my guess at how it'll work, there's any number of ways they could do it though. It'll be interesting to see how it's done, there will certainly have to be a new system from M2TW to incorporate the new features. Hopefully it'll allow for modding in all sorts of interesting emergent factions/unique rebels.