You have to be able to “turn off” the transponders for a lot of sensible reasons:
1) When the plane is on the ground, say at the terminal, or in a hanger, you need to be able to turn the transponder off
2) In the case of an electrical fault with the system, you need to be able to isolate the system to prevent fires etc
3) During maintenance etc, you need to be able to remove power from the transponder to allow that maintenance.
4) ATC might want the pilots to disable or change their transponder settings during a flight etc
The thing is, if you can’t “trust” the pilots, then what use are any “safety” systems on the plane? I mean, they can still fly the thing into a mountain quite easily. The entire system revolves around trusting the pilots, and if you can’t do that, well, what’s the point?