I'm not suggesting that this is something that should ever happen without the user requesting it; they (or an administrator) would have to add a folder to a .conf file (either manually or via a right-click menu) to flag that folder for automated cleanup.
Then, the next time an Update is run, in the list of pending changes would be all the files that meet the cleanup criteria and are pending deletion. The user could then uncheck those that they want to exclude from the action.
I understand your hesitance at deleting a user's files (I had the same initial reaction to the idea), but keep in mind that these are files that are already safely stored in the repo so nothing will be lost.