Previous to today, using SQL 2008R2 as a back end database instance for the Operations DB, Warehouse DB, or SSRS reporting instances was not supported.
Over on the MOMTEAM BLOG and in KB2425714, they just published a support statement for SQL 2008R2.
This is being handled in two phases:
Phase 1: New installations of OpsMgr 2007 R2. This is supported as of this writing, using special steps outlined in http://support.microsoft.com/kb/2425714 Note, there are some special steps to get this working, and there are some known issues with no workarounds if you must use 2008R2 at this time.
Phase 2: Upgrading an existing installed management group from (SQL 2005SP3 or SQL 2008SP1) to SQL 2008R2. This is NOT supported/available yet. This is the process to upgrade your existing management group database and reporting instance roles to SQL 2008R2. This is planned for a future CU (cumulative update) which will add support for this process.
*** NOTE for ACS: While the KB above does not mention it – ACS is also supported for NEW installations of the ACS DB and reporting website, on SQL 2008 R2. UPGRADE of an existing ACS environment to SQL 2008R2 is not yet supported, consistent with the OpsDB, Warehouse, and reporting roles.