Hello sobrog, Immunet can be used with Windows Server 2003 & 2008. You'll have to write your own install scripts as far as a batch install is concerened. Although Immunet will give you additional features compared to just using ClamAV, such as two additional cloud based detection engines & more advanced heuristic capabilities plus the incorporated ClamAV detection engine, there are still limitations as far as customizing the software to suit your multiple endpoint needs. For instance, compared to ClamAV there is no automatic command-line scanning feature with Immunet. Also, some users have reported Name Resolution conflicts while using Immunet within a server platform.
One additional option at your disposal is to use FireAMP instead (this is the Enterprise version of Immunet). This security solution has been designed from the ground up to work in a multiple endpoint enviorment. Although not free, it is highly customizable, easily deployed within an enterprise infrastructure and will provide you with many additional security options compared to Immunet. More info about FireAMP can be found at the link provided.