Do you have a SQL 2012 Exemption for the process. You might not have a predefined process:
First Select the Endpiont Protection SQL 2008 and click copy
I name mine Endpiont Protection SQL 2012.
Edit the Exclusion Settings in your new Policy
You will need to make sure you modify all the appropriate paths for SQL 2012:
Also, make sure if you have an Instance name that you add that to the path for SQL.
Note the addtion of :
%Program Files%\Microsoft SQL Server\MSSQL11.CONFIGMGRSEC\MSSQL\Binn\SQLServr.exe
This is to ensure all Secondary servers are not affected.
This should be similar to your ConfigMgr 2007 exclusions as well as the SQL 2008 exclusions already contained in ConfigMgr 2012.