We had a user accidentally clear out a shared folder as a part of clearing out the rest of his owncloud folder. He also deleted the "Deleted Files" cache.
There should be an extra warning for shared folders in the UI.
"You're about to delete the contents shared by others. This will delete the file in other people's shared folder. Are you sure you want to do this?"
Or alternatively, only Admins of a shared folder would be allowed to permanently deleted shared files.
This is a serious design flaw which compromises the value of file sharing in owncloud.