Although I do agree with your point that the risk there is different; a much easier control would be to have an emergency autopilot mode in the plane that the pilot can't disable. So if the plane gets hijacked ... it just flys its normal route. The hijacker's only options are to either kill everyone on board (same risk profile as a bus trip) or not (at which point they aren't effective hijackers).

Even if the plane just downed itself in an ocean in an emergency; that'd be technically not so hard to pull off. Enough to deter hijackers so the mechanism wouldn't need to be used.