One option to killer stacks is some sort of local supply rating, perhaps with buildings/improvements/spells you can use to help that out. A big army takes resources to maintain in the field. You can port all those with you or forage from the surroundings.
I can see "porting supplies" in the form of caravans of supplies having to be purchased or some sort of production penalty to nearby towns if you exceed their supply. Which in turn means your inherent supply is better near your towns than in the midst of an enemy.
It would also place emphasis on quality versus quantity. Say it's cheaper to build a powerful stack of cheap units, but the supply issue can be crippling if it gets away from the premium supply zones. Where as that really expensive to create stack of elites doesn't have a supply problem, but takes longer to build and costs more.
I wouldn't want to delve too far into an entire supply economy, but I can certainly see the idea of supply caravan units supplying an army. Either prebuild enough for your army's trip or wagon train them there and risk your supply line being intercepted and killed. That would certainly make fielding a killer stack a more significant strategic effort.