Could you not create a quick script to do this? The mailboxes would be in standard stores, so have a series of scripts that would clone each store as required. If you put in a pause in the script, then when the operation is complete, continue and the clone gets removed.
You could use RBAC to create a specific user for this sole purpose, and then use either RSH or SSH (SSH always my preference). Let me know if you'd like some examples and I could email some stuff across.
The difficulty is limiting access if you are using SMBR to recover the mailboxes however.