Who was responsible for auditing DHS computer security?
It's not clear from the article what was compromised; for example desktops or servers, or both? Were the machines behind the corporate firewall or in the DMZ?
DHS ought to have an independent security officer whose job it is to do a comprehensive security risk analysis and a thorough compliance audit, especially where contractors are concerned, to ensure that standards are adhered to and maintained. The responsibility for ensuring this happens lies squarely with DHS senior management. Vigilant, independent scrutiny of contractors is a basic 'must-have' where strategic IT is outsourced and contractor incentives and penalties must be appropriately aligned to prevent commercial interests from compromising quality of service.
Desktops running Windows are especially vulnerable. For handling sensitive information, thought should be given to systems which are easier to secure and present more difficult targets for hackers. In any case, steps should have been taken to ensure that the compromise of a desktop does not necessarily lead to the theft of information.
Having network intrusion detection is good, but security should be multi-layered and the set up provided by Unisys, for whatever reason, was clearly unable to prevent the theft of important information and the misuse of DHS assets.