How to switch from Spotlight to Alfred via Terminal?
Alfred requires Spotlight to function properly.


  Alfred relies on the same OS X metadata index as Spotlight. As such, it's important for you to let Spotlight run on your Mac to maintain an index of the files on it.


http://support.alfredapp.com/kb:spotlight

This answer to a similar question provides a shell command to stop Spotlight's GUI only, which will disable Spotlight's shortcut.