You could create a player upgrade, similar to the existing HQ upgrades, that is required by certain player upgrades, which you would add to the army's list of abilities.
The only way to disable commanders is to use a Win Condition Pack, and change the following line in your .win file:
permitted_categories = commander + intel_bulletin + skin_pack + vehicle_decal + fatality
to permitted_categories = intel_bulletin + skin_pack + vehicle_decal + fatality
Hm. I am working on a propert bag, so it'll be a problem. There's no way to just disable the spawning of the commanders' items?