Thanks to Dave Howe for pointing out this newly released hotfix. With the release of KB.883652, it’s now possible to script cross-site mixed-mode moves based on the Exchange 2003 SP1 feature. Before applying this hotfix, if you are doing scripted moves with the MoveMailbox method of the IMailboxStore interface and you select a destination in a different site you will get an error like:

This mailbox cannot be moved to a different Exchange Server 2003 administrative group while in a mixed Exchange 5.5/Exchange Server 2003 Organization.
Error code: -1056749031

With the hotfix in place, a new parameter (FCrossAG) is exposed that allows you to specify that the move should be cross-site. Also included with this hotfix is exposure of a parameter that allows you to control the Skip Bad Items feature of Exchange 2003 mailbox moves (IMaxBadItemsToSkip).

Please see KB.883652 for more detail on how to use these changes and download the hotfix here.