I think there’s a pretty good chance your stick shift saved your car. Chances are it wouldn’t start because the thief didn’t know about the clutch safety switch, and didn’t know he would have to press the clutch to get it to start.
While it’s true a professional thief wouldn’t have been stopped by the manual transmission, a lot of car thefts are perpetrated by amateurs who don’t know what they are doing and are just looking for something to take for a joy ride or to use it to commit a crime.
If you don’t intend to fix your ignition switch, I would add another measure that might deter an amateur thief, like a locking anti-theft device on the steering wheel. If you get something like the Club, putting it on backwards, so the lock faces the dashboard instead of facing the driver, can work. However, I would get the switch fixed, especially if you have theft insurance; that’s what it’s for.
I realize there is nothing I can do to stop a professional thief who knows what he is doing, but that doesn’t stop me from taking measures to deter low rank amateur thieves. I figure real pros would want nicer cars than the one I drive. Besides, if a professional thief steals my car, I’ll probably never see it again. If an amateur steals my car, the police will probably find it crashed in a ditch, and I’d get back a car I no longer want.