I haven't removed one in a while (or under the new SDS model), but you should be able to delete the users from that site to remove them from the Tel Dir and then get rid of the CEID routes in ARS, IP trunks and then the two cluster forms.
Just as a warning it was normal for the network elements form to still have the PBX number there after it had been deleted. All of the information associated with it would be deleted but the PBX number would stay.