I agree that lots of small-scale fights with irregulars and having to hunt down M2TW/RTW style rebels and brigands isnt much fun( and these guys wouldnt be willing to stay in the field and be hunted down anyway), still guerilla, freikorps and cossacks performin ambushes, raiding supply trains and such were a part of the eras warfare, and these things should have an impact one way or another.

having them represented by losses of resources and men in the areas where they are active sounds good to me, and maybe one could counter them by assigning troops to counter-insurgency duty for a period.