DmdNexus,
That is EXCACTLY what should be happening if you follow the CHI (Computer Human Interface) standards for a GUI.
When an issue occurs with your operation, and a 'standard' response is available (operation = fly, issue = not_enough_fuel, standard_response=load_available_fuel) then the GUI interface SHOULD provide that as an option. We would get 2 options presented to us, Fly_with_Available_Fuel, and Cancel. The same would go for drop_tanks and ordnance (HAH, y'all though I was going to say ordinance didn't you!).
Now, putting this in would require a bit of work (setting up the flow of the operation so that as each issue is hit, a new window would pop up), but when they get done with everthing else, this should go on the list.
Ouch out