I admit I have no idea how the system works but if there is an obligation to submit a flight plan in advance then there should also be a standard procedure not to let planes take off or enter airspace if they don't. At the very least there should indeed be a procedure to reject the flight plan even if flight cannot be stopped.
Airspaces are already a thing in aviation, and pilots need to seek permission to transit between them. This is done by making the request to air controllers via radio.
