Particularly this question is focused for Windows Server 2008 R2.
I know the registry can be used to modify particular entries to disable weak ciphers if they are known.
I saw this tool: http://www.defensia.co.il/2011/05/12/hardening-iis-ssl-with-iiscrypto-disabling-weak-ciphers/ but I'm not familiar with the creator so I'm not too trusting of it.
I'm sure there may be a template to use of some sort, but I'm not familiar with the exact details of that.