Shouldn't be a problem. Won't damage a controller unless it's defective anyway. You will experience some resistance, and the faster you pedal the more the resistance will seem to incerase. You won't be going fast enough for what AW was talking about. I've coasted down some big mountain passes without damaging controllers.
Also, you could just unplug the controller from the motor. Nothing bad could happen then except for the motor wheel coming loose from the bike if the nuts aren't installed correct.
If you have a short in the phase wires, you'd have a LOT more resistance. So that's one way to check for a shorted controller. Plug it into the motor and if it's resisting more than before, the controller has shorted a fet.
You can "lock" an ebike, by unplugging the controller and plugging in a wire that deliberately shorts the motor phase wires. With the plug in place, it will be incredibly hard to ride it away.