No, your "Macintosh HD" volume won't be repaired if you click repair on the actual disk. In the Unix world, people usually have a lot of volumes, so everything is always quite specific in matters like this one.

There is no 'G5 intel' Mac, do you mean the Mac Pro? Also note that G5s can't run OS X 10.6.

That is weird. However, it does make sense, as the preferences are stored in that file, and that file doesn't exist on your computer. You can download an empty .plist file from dropbox.com/s/z1xb9lj0t7j3y9l/com.apple.Safari.plist , and place it in your ~/Library/Preferences folder.

Are you ok with installing a little third party utility to run an Apple script when a keyboard shortcut is pressed?

Try booting from the Recovery HD and see if the button is still disabled.