Can the Growl update message be stopped without removing Growl?
From the Growl FAQ page:


  How do I disable the update checker in 1.2.2 and below?
  
  The update checker in Growl 1.2.2 and below will run automatically every 24 hours. The update checker in 1.2.2 admittedly is not great, and is one of the reasons that Growl is now in the App Store. 
  
  For those who wish to continue to run Growl 1.2.2, you can do so but will likely benefit from disabling the update checker. 
  
  To disable the update checker, follow these steps:
  - Open System Preferences
  - Click on Growl
  - Click on the About tab at the top
  - Please make sure that you are using 1.2.2. If you are not, please update to 1.2.2 available here
  - Uncheck "Check for updates automatically"
  - Close System Preferences, you are done


Since the older version is going to become less compatible over time I would honestly suggest just paying the $4 and upgrading to the latest version that integrates all Growl notifications into message centre, even for apps that don't support message centre.