The rebel armies that form are mostly made up of militia (from my experience at least) and can be beaten fairly easily with your invasion force, provided you use the nifty replenish feature immediately after taking the region, or didn't lose that many men in the first place. With larger cities like Warsaw, though, your force may get stuck in the province for a few turns regardless. I always repair the governor building right away and build bawdy houses in really troublesome regions.
I think it's good that this at least to some extent puts a damper on blitzing.