Although not practical in this day and age, AI Pilots would solve many of these problems. Instead of moving the pilot to a secure location, and using Remote Control, why not just skip the pilot, and have an on-board computer (locked securely away, of course) do all the navigational work.
The computer would have access to weather, GPS and other navigational data. Also, an emergency code changed every flight, and known only to ground control could be used to force the computer to land the plane. The issuer of the code would have no control over where the plane would land, just the fact that it would land ASAP.