I don't know how good you are with electrical, but a hidden master switch isn't a bad idea. Make it easily accessible but not easily found. If you don't hit the switch, nothing on the bike gets power. You could also do something as simple as loosening the plug wire.
It also can't hurt to have some 'hidden' identification markings on the bike incase it does get stolen, you can tell police to look for the markings you made.