Currently military power of havens adds up from 1) haven population, 2) training facilities and 3) nearby havens.
My suggestion is to add +3 military power if the haven has an aircraft stationed in it.
Proposed results:
1) Player would be a little bit less motivated to steal an aircraft knowing it is going to undermine that haven's ability to defend.
2) Faction aicrafts moving across the map would be less meaningful and may be seen by player as relocation of faction military power.
You may say that the aircrafts are unarmed in the current version of the game, so they can't be seen as gunships. However they can surely be used as scouts and to deploy and evacuate soldiers at battlefield, so they can still contribute to battle in some ways.