Hi,
I would advise you to install only AV/AS (Anti-Virus & Anti-Spyware) and PTP (Proactive Threat Protection) on your Windows Server 2012 with SEP 12.1 RU2.
You should be fine with that.
There is a new version of CleanWipe way more easier to use and way more nicer than previous version.
Easy to run, you can pick what you would like to remove (SEP client software only or Windows LiveUpdate or Management Servers or all of them depending your needs and recommendations).
If you need it, log a case to the support.
Kind Regards,
A. Wesker