The SEI is located like a half-mile from the main part of the campus of the school (it's basically on the campus of University of Pittsburgh). Some of the professors in the CS department might work under SEI grants, but yeah, the SEI is basically an independent research organization that is heavily government-funded (like almost every research institution). They do a lot of non-evil things too, especially related to the challenges of building and maintaining extremely large applications (and the organizations that build and maintain them).
Fun fact; their building was used as a police station in The Dark Knight Returns.