就地升级Windows Server 2012到安装了System Center和SQL Server

Configuration Manager supports installing System Center 2012 R2
Configuration Manager to upgrade a site that runs Configuration
Manager SP1. You can run the upgrade on the site servers of central
administration sites and primary sites. After a primary site upgrades,
you can then use the Configuration Manager console to upgrade
secondary sites to System Center 2012 R2 Configuration Manager.

http://technet.microsoft.com/en-us/library/jj822981.aspx

更新的答案：

Window Server 2012到Window Server 2012 R2正式支持就地操作系统升级

Updated details for the in-place upgrade of the site server operating
system. Windows Server 2012 to Windows Server 2012 R2 is supported.

http://blogs.technet.com/b/configmgrteam/archive/2013/12/19/announcement-configuration-manager-documentation-library-update-for-december-2013.aspx

全部细节：

Configuration Manager supports an in-place upgrade of the operating
system of the site server in the following situations:

• In-place upgrade to a higher Windows Server service pack as long as the resulting service pack level remains supported by Configuration
  Manager.
• In-place upgrade from Windows Server 2012 to Windows Server 2012 R2.

Configuration Manager does not support the following Windows Server
upgrade scenarios.

• Any version of Windows Server 2008 to any version of Windows Server 2008 R2 or later.
• Any version of Windows Server 2008 to any version of Windows Server 2012 or later.
• Any version of Windows Server 2008 R2 to any version of Windows Server 2012 or later.

资料来源：http://technet.microsoft.com/en-us/library/gg682077.aspx

附加信息：

有些用户可能会发现此链接也特别有用：
Upgrade Sequencing for System Center 2012 R2