We absolutely need the ability to merge organizations much like you would merge users or tickets. It is not uncommon for one of our customers to acquire another customer or for a company with two different business units that had separate purchases to ask us to merge their accounts and manage as one unit. Zendesk does not seem to offer the ability to merge at this level.
One possible (but ugly workaround) is to re-link all users from the disintegrating organization to the surviving organization and then either "delete" or somehow mark inactive the account that is being consumed. Zendesk should provide this capability with the full understanding that all activity and history is merged and only one account will survive at the end.