@Klaykowalski
On page 5, of the partisans rulebook there is a box that states what partisans are not. One of these is that they “are not counted as regular land units for any reason.” I interrupt that as meaning they do not receive a defense bonus, unless they are specifically mountain partisans.
As attacking penalties, infantry and cavalry are still subject to attacking penalties such as river rules. However, river rules apply when a unit combat moves into a zone. So a solution to avoid the penalty it to noncombat move into the zone and attack the partisan on the following turn. That is how I have been handling the terrain bonuses/penalties.
As for the resource disruption, the partisans only succeed on a 1-3. So you have multiple partisans in a territory to get above 3 IPP loss. I would think that you couldn’t lose more than the territory is worth though, similar to convoy raiding. It doesn’t state that in the rules.
As far as killing partisans, remember that all partisans actions have a failure value. If the partisan rolls that number they are eliminated. Cavalry and infantry can attack partisans, so you have to have several units to increase your odds of hitting them. They are not supposed to be easy to eliminate (between being attack by low % units and their fade ability.)