Q: How do I remove a site system role from a server in System Center 2012 Configuration Manager?

A: Removing a site system role from a server in Configuration Manager 2012 is actually a very simple process but initially is so obvious you can overlook it! In the Administration workspace, navigate to Site Configuration, Servers and Site System Roles, and select the server from which to remove the role. 

Then, at the bottom of the screen in the details area, select the role you wish to remove, right-click and select Remove Role.

You might also look at "Q: My Configuration Manager 2012 client isn't correctly receiving policies--how do I force the client to delete all its policy and download again?"