How would the system determine it is in-flight and thus prevent a maintenance shut down? You would need another device to determine in-flight from ground operations, and thus another device that can malfunction and thus can be defeated by an attacker.
>Give me any reasonable response to why this is not something that should be fixed.
Give me a reasonable response why spending a bunch of money to fix this rare issue is worth it over other safety improvements? Old aircraft, poor maintenance, and overworked pilots kill many times more people than hijackers.
P.S. Why don't we track buses? Why don't we track cars? Why don't we track everybody?