In-flight decisions are an ongoing process.
For instance, I have twice been told by ATC to turn around and go back ... What would a computer have done?
How will a computer handle a military interception? Climb, descend, turn?
As is frequently pointed out in this forum, an aircraft's commander is responsible for its safe operation and not only is entitled, but has a duty, not to do what ATC says if the situation merits. An artificial-intelligence 'captain' of an autonomous aircraft would surely have the same authority. An aircraft that can be controlled by ATC wouldn't be an autonomous pilotless aircraft but a piloted UAV with ATC having the command responsibility.
A military interception is a bit different. Then the AI 'captain' would have to be able to understand that it's being intercepted, understand commands from the interceptor and do what it's told. Alternatively the interceptor could be equipped to take control, so that the aircraft again becomes a piloted UAV with the interceptor having command responsibility.