Perhaps I'm not clear enough then. They don't have to do either. The relationship data is cleaned up by Pulp, which is what I was referring to with "When a user unassociates units from a repository, the Pulp server will make the necessary database changes to reflect the change.". This was initially added as a hook so the yum importer could delete the symlinks it was maintaining in its working directory, which is what I vaguely alluded to.

I'm open to suggestions, I'm not sure what changes to make.