When I go backpacking and park my 2006 prius at the trailhead I disable the Smart Key with the under-dash button and leave the fob in the car, taking only the small physical key in my wallet. I'm afraid the fob could be lost or damaged on the backpack. Now with my new plug-in, I don't see a way to disable the system so I can lock the fob in the car. Am I missing something? Anyway to do it short of removing the battery from the fob?
Yes, via the vehicle customization menu per the Owner's Manual pg. 639-640. The instructions are different depending whether you have the Display Audio or Premium HDD, so you should refer to the appropriate manual.
Or do what I do and just keep an Altoids container in your car and put the FOB in it while you're out of the vehicle and keep the mechanical key with you.
I keep the fob with me while backpacking, personally. My backpack has a zippered interior compartment with a hook for keys, so I figure that's protected enough that I can't lose or damage the key.
I place the fob in the center console and use the mechanical key to manually lock the doors. This seems to disable the key fob until the door is manually unlocked with the key.