the transponder is not some magical homing beacon. it has multiple modes and it can be turned off when it's not needed.
i'm not sure what you think the transponder does but it's not a very special piece of equipment.
if the plane were hijacked there is a special transponder code the pilots can use to indicate the plane is being hijacked. so obviously the pilots / pirates / hijackers with knowledge of the airplane were careful to avoid that situation.
why shouldn't a pilot be able to turn off aircraft systems
what if your plane was about to catch on fire and the only way to stop the fire was for the captain to pull the fuses for the electrical system causing the problem? sure would suck to die because of a restriction put in place due to media hype.
