Support for installing Microsoft Windows Server IA64/Itanium with System Center Configuration Manager with Forefront Endpoint Protection (FEP) is as follows:
System Center Configuration Manager 2007 supports Microsoft Windows Server 2008 R2 IA64 (Itanium)
System Center Configuration Manager 2007 supports Microsoft Windows Server 2008 R2 x64
System Center Configuration Manager 2012 supports Microsoft Windows Server 2008 R2 x64
System Center Configuration Manager 2012 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)
Forefront Endpoint Protection 2010 supports Microsoft Windows Server 2008 R2 x64
Forefront Endpoint Protection 2010 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)
System Center Endpoint Protection 2012 supports Microsoft Windows Server 2008 R2 x64
System Center Endpoint Protection 2012 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)
System Center Configuration Manager 2007 supports Microsoft Windows Server 2008 R2 IA64 (Itanium)
System Center Configuration Manager 2007 supports Microsoft Windows Server 2008 R2 x64
System Center Configuration Manager 2012 supports Microsoft Windows Server 2008 R2 x64
System Center Configuration Manager 2012 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)
Forefront Endpoint Protection 2010 supports Microsoft Windows Server 2008 R2 x64
Forefront Endpoint Protection 2010 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)
System Center Endpoint Protection 2012 supports Microsoft Windows Server 2008 R2 x64
System Center Endpoint Protection 2012 does not support Microsoft Windows Server 2008 R2 IA64 (Itanium)