The situation seems to be relatively complex due to what you're asking for, applegeek -- SD! is more than happy to do what you want on a regular basis (say, late at night), or to sleep the system with the drive connected. It does stink that Apple manages removable drives poorly -- Windows allows them to be disconnected without fear of extreme corruption -- and we've tried to help with the mount/unmount behavior of scheduled backups, but cannot currently combine the behaviors.
You could write a little shell script that would eject your external drive after the backup, and set that as the "after copy" action if you'd like. That little script could even then put the system to sleep... but I'm reluctant to add additional complexity to SuperDuper! for a case that doesn't come up very often -- that way lies Retrospect.
