i think the issue is the other way around. plane crashes arent integrated ENOUGH into the game. all aircraft abilities need to include choosing the flight path of the plane, That way you can try to avoid your plane flying over where you think AA might be. Also if the plane crashes youd know that itd crash somewhere along the flight path.
This also has the added benefit of developing a meta game around air flight paths as the other player would actually have to think about where the flight paths might be and position his ostwind/whatever accordingly to shoot it down.
Right now when you call in air, planes just come from random directions and pass over the targeted area. so planes getting shot down and crashing is just totally random in all categories. there could be so much more interesting air meta game.
What you say makes sense, but that does not solve the problem. First of all, you don't have to option to "not fire" at the enemy, when you bring an Ostwind or AAHT, the fire at the enemy aircraft. Second of all, the issue still remains. You get punished for killing an enemy unit. I don't wanna exaggerate, but I have lost A LOT of units because of that.
So what you suggest is cool and needed, but that does not fix this problem.