I would assume that the fighter pilot can visually check that the cabin is secure and the crew are indeed in charge of the flight.
I would also assume that if the aircraft varied from instructions given to it and for instance decided to crash dive into some area or other such as a nuclear power station then it might be shot down.
It may be a little naive of me, but I am assuming that there is an understood protocol in these cases. Unfortunately, as it is, I assume, a military protocol, we won't be party to it, but it would be comforting (or not!) to know what the sequence of actions actually are.