How do I completely unpublish a node (not just change revision state) when using Workbench Moderation with rules?
Well, I suppose it's a bit late, but this issue is discussed in and should be mostly solved by https://drupal.org/node/1436260 once the issue is fixed. You should be able to unpublish the node, and as long as the code calls node_save, workbench moderation should set the state back to draft. If you want a different state, e.g. "archived", you'll probably have to come up with something custom.