Does a 3-winding common mode choke work on PE wire
I would first attempt to improve the integrity of the PE connection path, either with a shorter/lower inductance path to ground, or a dedicated "functional" PE.  If that doesn't suffice, then I would consider galvanic isolation in your sensor path.

Common mode voltage becomes a problem only when a secondary potential exists to turn it into differential mode voltage.  Consider the lineman working on a 110kV transmission line from a helicopter.  He's at a common mode potential of 110kV; his bigger safety risk is rotor failure.