If you're interviewing candidates and you have a candidate graduating from Stanford, one from MIT and one from Middle-of-Nowhere State - which candidates are you going to prefer? We can argue whether such preferential judgement is justified. Living near the East Coast I can tell you I've met my share of MIT grads who are idiots and Middle-of-Nowhere State grads who've been really good. Yet the perception persists. Why? Because of the handful of truly outstanding, even legendary, graduates the elite schools have had that Middle-of-Nowhere State hasn't. Those handful of exceptional graduates skew people's perception of reality for a really long time.
Who knows? Maybe this scandal will change people's perception of these elite schools but I doubt it.