Flight delays / cancellations / diversions (due to mechanical problems, weather, etc.) are a very regular thing - the airlines, ground crews, commercial pilots, and control towers have lots of experience with "Flight 1234 won't be taking off..." and "Flight 2345 is being diverted to...".
Or, if it's a "Bob owns a Cessna, and took off anyway" situation - well, Bob's license to fly a private airplane will probably be taken away. Maybe his Cessna, too. And (post-9/11) Bob could be spending some time in uncomfy little rooms with bars on the windows.
To add, my personal experience from the air force is that flight plan rejection from Eurocontrol was business-as-usual situation so I'm also confused reading that the system instead of rejecting that one problematic plan, threw a white-towel
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.
Or, if it's a "Bob owns a Cessna, and took off anyway" situation - well, Bob's license to fly a private airplane will probably be taken away. Maybe his Cessna, too. And (post-9/11) Bob could be spending some time in uncomfy little rooms with bars on the windows.