I wouldn't worry so much about the motor. These are pretty well sealed coming from the manufacturer. My bike went through some serious torrential rain, hosing down and even buckets of water being splashed on it from above and it is fine. The only item on the bike that experienced any water damage was the throttle.
Both of my Crystalyte motors had Hall sensor problems due to moisture. I switched to sensorless controllers, aka "Pedal First" controllers, and they run fine even with the moisture inside. This is a common problem in the Seattle/Vancouver area.