Adding a relay to stop motorcycle engine
A CDI usually has two inputs. The first receives several pulses of some 100V to charge a capacitor, the second is a trigger signal of just a few volts to discharge the CDI via the primary side of the ignition coil.

So, if you want to place your relay here, you should switch the trigger. Remember that the charging and trigger pulses come from a generator like setup, if you open these circuits, you may get high voltage spikes. So, you may ground the trigger signal via an appropriate resistor.

However, the motor is stopped by the key, so why don't you switch the wire from the key?