I have the Stoker, but I have the same challenge with rain. I bought a medium-sized plastic storage box...shallow, usually for storing clothes. It has a tight-fitting lid. I cut a couple of slits on the side for my probes, and on the other side for the power cord. With the lid on the box, this thing is essentially water proof. I usually throw the cover for the WSM over the top of the whole thing and weight it down (in case of high winds) and it is good to go for protecting the controller.
The fan is another story. I usually take a sheet of aluminum foil and attach it where the fan goes in to the WSM, and drape the foil over the fan, making sure the foil doesn't impede airflow.
I always protect my Stoker, even if no rain is predicted.