To be honest as its not worth the effort as people can just view the main page and get the html for the footer and then paste it into the footer.php and now its not encoded. If you make require say a certain url to work then they can use the same method and wrap <!-- whatever link here --> then the script sees it then the desing works and it still doesnt show the footer links on the site.
So much like a car alarm it will keep honest people honest but a thief is a thief and will get around it. Plus people are getting keen that big "G" doesnt like sites with the sponsored links in the footers.
Here you can input the code and encode it if you like dean.edwards.name/packer/
As you can see on the same site the option to decode it also all though it looks like its disabled its not you need a FF plugin to make it work.