The exclude option of rsync works on relative paths not absolute ones. So for your example something like the following will work:

rsync -avz --exclude 'directory' source_directory/ destination_directory/

In this generic example you can see that --exclude 'directory' assumes that directory is a sub-directory of source_directory.

I have included the -z option for the rsync line, compression gives a few small speed increases...

Notes:

• How to Exclude Files and Directories with Rsync: The page that got me to finally understand the --exclude option of rsync :)