I'm not sure we should design this system on the assumption that we suck and will probably blow things up. I don't know of any other programs that use such a mechanism when upgrading!
Well, Service Packs on Windows have the option (on by default) to back up all changed files just in case Microsoft suck and blow things up; a Wine upgrade could be considered roughly equivalent to installing a SP if the gap between versions is big enough.
Perhaps backing up the old wineprefix and telling the user that it's been upgraded would be a good idea. Will the wineprefix be upgraded with every new Wine release, or just when something actually has to be changed?