The WSUS team announced that System Center Virtual Machine Manager 2008 R2 will be added as a new product in WSUS. This was announced a few days ago. I haven’t checked yet but it has either happened or will happen soon. They did say “near future”. Make sure you add it and do all the usual tested before deploying updates.
I know I missed a fix for VMM 2008 when I didn’t add it as a selected product in our WSUS installation. And that was a fix I wanted too.