Is it easier just to copy the exploded deployment and have the scanner keep the copy in sync. I've done that for farming; it's not such a big deal. I'm starting to feel like not doing that is leading to a lot of internal complication (e.g. needing to keep track of multiple locations where content is stored.)
That doesn't solve the atomic move problem, but maybe if people can't do atomic moves they should use the filesystem as their deployment API. :)