Microsoft has released a new cumulative update package (CU7) for SQL Server 2008 R2. The build number is 10.50.2817.0.
You can request the update here: http://support.microsoft.com/kb/2703282/.
Normally Microsoft don’t announce if Configuration Manager and other System Center product has support for Cumulative Update (Only Service Packs), so this update should be fully supported by System Center 2012 Configuration Manager.
Don’t forget to test it in your lab first… 🙂