With that amount of files being infected I would highly recommend that all computers be reimaged along with the servers. The files may be able to be cleaned but they could also end up corrupted. You need to have some policy in place to stop files being downloaded from the internet, as that is where they have come from. Someone probably used a torrent for a cracked programme and it just went rampant throughout your system. Also you need to ensure that no-one apart from the system admin can turn off or disable any part of the Antivirus