Instead of triggering a SUP sync after publishing, create a one time scheduled SUP sync.
One of the features of running a scheduled SUP sync is the cleanup process that follows. The current option in PatchMyPC to trigger the SUP sync is not considered a scheduled sync so the cleanup does not occur. The PowerShell cmdlets are there for creating a non-recurring one-time scheduled sync in order to get the full functionality of triggering the SUP sync and getting the cleanup features too. Perhaps even having a timer option (in minutes) to set the one-time scheduled sync once publishing is complete.