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.

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.