PackageKit is the graphical tool that alerts you when updates are ready. It's triggered by the "refresh-packagekit" plug-in (see the second line of your quote). Not sure if you can disable it, but just waiting a few moments should avoid the issue.
Are you using a graphical desktop environment (like Gnome or KDE)? If so, look for the PackageKit icon in the notification area (in Gnome, it's in the top-right by default). Have you ever seen a pop-up saying there are updates ready? This is PackageKit. It needs to be refreshed each time something happens with yum so that it can display correct informations.