I just would like to point out that you could simply write a tiny plugin with this code:
function relativePathForUploads($fileInfos)
{
global $blog_id;
$path = get_blog_option($blog_id,'siteurl');
$fileInfos['url'] = str_replace($path,'',$fileInfos['url']);
return $fileInfos;
}
add_filter('wp_handle_upload', 'relativePathForUploads');
That will store all uploads as a relative path.
*tested on MU 2.8.6