The easiest is probably to wire a hidden momentary push button into the clutch wire. That way you have to press the button, while holding the clutch down and turning the key. Costs about $1 to wire in, and the way I see it, the average thief isn't going to hang around for more than about 30 seconds when they can't figure out why your car won't start.
Or, if you're really paranoid about it getting stolen, I suppose you could flash a map to the ECU that wouldn't allow the car to start. I don't care how crafty a thief is, if the ECU doesn't dump any fuel they aren't going to be driving the car away.