It seems that currently the Organizational items (department, cost center etc.) deactivation doesn't and that may will be a use case on its own but I think it would be sensible to hide disabled organizational items from various assignment lists (for example on creating a new external identity manually you could not add a disabled department as his primary department through the master data view).
Some organizations may have a need to still see disabled departments/cost centers/ locations/ business roles on various lists but I would suggest adding a simple option to hide disabled organizational items from lists.
Of course it is not overly complex to do this in each implementation where needed but this was a enhancement proposal from one of our customers that I promised to push to the community.