Leaving the system empty won't do any damage. The drain bolt should be at the lowest point in the system and normally on the left side, so that with the bike on the side stand, the radiator drains downhill. If you have the bike on a paddock stand, tilt it side to side with the drain bolt open to encourage more of it to get out. Whatever remains in the system in minor low pockets won't be a problem. It's like an ice cube tray in your freezer - the water has a place to go, so it doesn't break the tray.
It's a whole lot easier in the springtime to refill it with water if you don't have to flush out coolant in the process.
DO put a piece of masking tape over the ignition switch with "NO COOLANT" written on it until such time as you refill it.
It's supposed to go below freezing this weekend, so now is the time to take care of this.