Change custom post type GUID in RSS

The feed template files call the_guid(), which calls get_the_guid(), which has a filter named (surprisingly) get_the_guid. You can hook into this filter to change the output. The filter only gets the current GUID, not the post ID, so look this up in the global variable if you need it.

add_filter( 'get_the_guid', 'wpse17463_get_the_guid' );
function wpse17463_get_the_guid( $guid )
{
    return 'http://example.com/guid/' . sha1( $guid );
}

See also this Trac ticket which proposes to change the current GUID format to a more unique hash.