“We should remove transponders from private airplanes as the occupants privacy is more important than the safety they provide” is certainly a plank someone could run on if they wanted to change the current laws.
Instead of removing transponders, perhaps just randomize identifiers before each fly, so individual planes cannot be tracked?
We all do it already with consent, using our phones.
Not everyone holds a cell phone onto them neither there's public data for the position of each one.