There are alot of ways this can be done, I mean look at how company of heroes did it, one moment a player has complete map control, the next minute they lose all of their income because they left their supply line undefended. Now they have to send some troops back to recapture the territory that was lost, during that entire time their economy is basically shut down.
For a game like this, as mentioned sieging a stronghold happens pretty much how realistic siege's happen. Lock the enemy inside their stronghold until their either surrender or starve to death. Assuming this exists in the game, the defending player could be aggressive and in turn attack the attacking players supply camp, destroying their field rations.
Basically I think the real suggestion here is how well can the espionage aspect of the game be. Kinda hard to sneak a loud army that marches through a forest rustling the tree's alerting the wildlife swinging their flags in the air trying to keep the troop organized, especially if all the enemy needs is one scout to see the army mobilizing. But take a small platoon specialized forces who stand no match for an enemy army, sneak past the bulk to perform a surgical strike on the vital supply rations the attacking army needs to continue the assault (assuming they haven't already taken your own food supplies)