I'd love to open up iTunes, but all my files are gone and I don't want it to sync with my iPod which is full of music. Is there any way I can turn the auto-update to manual with Applescript?
Not sure how to do what you're asking with AppleScript, and I'm actually not sure it's even possible. But if you want to restore your iTunes library from your iPod, maybe try Ollie's iPod Extractor.
What do you mean that your music is gone? Did you actually delete it or lose it in some other manner, or did you open up iTunes one day and not find it? If the latter, then it can be fixed directly in iTunes from the Preferences -> Advanced pane.