Hunh? I've had an archive option in OS X Mail since (I think) 10.8. Message->Archive. Or Command-control-A. Or there's also a toolbar button to do it (you may need to customize to get it, though, I don't recall if it's there by default).
That still doesn't solve the fact that pressing delete will send to trash instead of the archive, in the past it just sent to the archive.
That doesn't sound like a problem. The delete button deletes and the archive button archives. Why would you want it backwards?