Detecting a break in continuity where no voltage drop occurs
Why not control a relay via a comparator, which changes state if the voltage on the battery itself drops, which is what would happen if the Controller was disconnected, ie normally closed relay, then if the comparator is activated, it opens the relay.

Edit:

Ok - to clarify:- 

1) Place a normally closed relay between the panels and charger, then use a comparator/opamp to drive the relay. 

2) The 'sense' inputs to the opamp come from either side of the Battery Cutoff switch, -ve to the battery side, +ve to the Charge Controller (CC) side.

3) If the Cuttoff switch is opened, the voltage difference activates the relay and protects the CC.

End edit.