I think it is pretty clear that you need a separate BES for Exchange 2007. We had not thought about this either but we are now as we are in the midst of planning our Exchange 2003 to Exchange 2007 migration.
If you have Exchange Systems Manager 2003 installed on the BES server it will fully support Exchange 2003 but won't fully sync with Exchange 2007 (e.g. Calendar sync doesn't work). If you remove Exchange System Manager and install "MAPI Client and Collaboration Data Objects 1.2.1" it will fully support Exchange 2007 but will have sync issues with Exchange 2003 (e.g. Calendar sync doesn't work).