How to disable shortcut for an Automator script?
If you want to remove the shortcut and not the service go to System Preferences &gt; Keyboard &gt; Shortcuts and make sure that in the right pane services is selected, I think that might have been your issue. The just un-click the check box next to your listed service.

I've had an issue recently where services aren't showing up in the services pane, to fix this just copy the service to your desktop from ~/Library/Services and delete the service in the Library directory, then paste the service back in again.