This seems a very odd outcome. After all the supposed changes post-9/11, I would think an international flight crew would need to be known to the destination and have entry clearance just to operate the flight.
Why not let the plane land, fine the airline, and detain the pilot in the airport until he can be flown back, instead of wasting hours of time of hundreds of people?
Because it's the pilot who makes the choice. Intentionally going to a foreign country without the appropriate documents is a bad idea with unpredictable consequences. Unless the destination country gives legally binding guarantees that nothing bad is going to happen, it's not something a reasonable person is going to do. Especially for a trivial reason such as work.