If it malfunctions you don't want it to overheat and burn the plane down. Thus the ability to cut power.
I'm sure the first battery meltdown/fire on a plane is going to cause a riot in the news but the odds...
I should point out that I don't know what is true. It just seems to be a contradiction that every passenger can take on board and use whatever they want in-flight, yet transponders specially engineered to be safe on a plane must be able to be disabled.
I suspect the answer is that the transponder doesn't need to be under the control of anyone on the plane.