They could make a computer lockout code to lock all access to All controls while the plane continues on the FMC programmed flight path. One that is randomly generated before every flight. The codes are kept by someone on the ground. In case of hijacking, pressing a special set of keys on the CDU or a special button would engage the lock. There should be a procedure drawn up to retrieve the code in case of false warnings. I suppose, on the new fly by wire planes, it should just be a matter of changing the software.