Adding this action to the check_ajax_referer hook will prevent saving meta box order changes from being attached to whichever user is logged in to the editor.

add_action('check_ajax_referer', 'prevent_meta_box_order');
function prevent_meta_box_order( $action ) {
   if ('meta-box-order' == $action ) {
      die('-1');
   }
}

This action can be added to functions.php or run from a plugin.