It's not very intuitive, but if I recall correctly, if you reset all per-repository permissions to "Inherit" they will be removed for a user. Try that, and let me know if it works.
In an early ICA-AtoM implementation, all notes were associated with users for accountability - even though this wasn't being shown in the user interface... which meant that you couldn't delete users who had notes in the system. The first compromise (rather than fully redesigning the implementation and migrating user notes, which would have been more involved) was to allow administrators to mark an account as inactive - this would be a way to disable the account without losing the user and their notes. In 2.2 we added a way for users to be deleted without affecting the notes. The internal relationships to that user will be removed, but in the user interface you won't really see any difference - the notes remain.
Let me know if resetting all custom permissions (e.g. archival description permissions, etc) associated with a specific repository removes the original repository affiliation.