You can reinstall WSUS according to the MDM Best Practices in MDM Deployment documentation. It’s listed under “Restart MDM services if you reinstall Windows Server Update Services (WSUS) 3.0 SP1”... but I've not tried it so I can’t confirm. Best to test in a lab first.
There is a Tech Note on the Migrating from Windows Internal Database to SQL Server 2005 process.
The process looks a little long but possible. The short option would be to reinstall WSUS and select a SQL 2005 Server during the install. You will then need to rebuild your packages using this method.
Cheers Wayne
Airloom