Q: Can I use SQL Server 2012 Standard Edition with System Center 2012 SP1 even though SQL Server 2012 uses per-core licensing?

A: The existing rights that were previously available with System Center 2012, namely the use of SQL Server Standard Edition to support the System Center 2012 management servers (but NOT for use by any other application or service), remain and extend to SQL Server 2012 Standard Edition with System Center 2012 SP1, which adds support for SQL Server 2012.

Even though SQL Server licensing changed with SQL Server 2012, it doesn't affect SQL Server 2012 Standard use for the exclusive use of System Center 2012 SP1 management servers.

As part of the System Center 2012 license, the customer has the right to use SQL Server Standard to support the System Center management servers. Remember, if you want to use SQL Server for more than just System Center 2012 purposes, you need to license the SQL Server instances per the usual SQL Server licensing.