Lets apply her reasoning to Ted Kaczynski (the unabomber). He received his undergraduate education from Harvard. He used the skills taught to him at Harvard to kill 3 people and injure 23. I have never heard anyone try to tie Harvard alumni in with terrorism but if people like Napolitano were consistent they would be just as hard on Harvard as they are the military. The reason she is not is because our military is a soft target and Harvard is not. Napolitano is anti-military, and a cowardly one to boot.
UPDATE: Here's the DHS's official statement.