Aussies are very velcro. They want to be with their people at all times. It may be a little late but crate training as early as possible is in my opinion the only answer to their loneliness. They will break your heart in the beginning but once established their behavior will likely improve. I know ignoring their pleading is difficult but they learn quickly if it is ignored.
Sorry that I don't have a better answer for you. I have had three Aussies and the last two were crate trained from weaning.