If I understand correctly, I think Powershell DSC (Desired State Configuration) might be able to do what you need with regards to windows server config.
Looks interesting, but our problem is more a separation of operation and development teams. It's not ideal, but we're a dev house and clients like to keep their operations in house for a number of reason (PCI compliance is one of them).
From my point of view OS configuration for app level concerns (web servers, services etc), should sit in the development realm, ready for operational teams to distribute and monitor.
Scripting systems does help, but it is not the final solution when you have mixed, varying talent teams. As a side note, every time I have tried scripting Windows systems I get an extra gray hair!
See: - http://technet.microsoft.com/en-us/library/dn249918.aspx - http://powershell.org/wp/2013/10/02/building-a-desired-state...