I would prefer to disable users that are no longer active instead of deleting them, at least for some project members that may return and then later delete the users in a batch (or you could just keep the users in the same state as autocreated users).
For this, a disable/enable switch in the user administration would be necessary plus probably checks if a user is active all over the place.

Another possibility would be to demote the users to autocreated and keep them in the database.