Because inaction in response to federal charges being brought against an unconnected individual outweighs more than 100 years of academic contribution.
I think this actually played into Swartz case. That possibly MIT didn't want waken a moral/ethical discussion around technology which is exactly what Aaron was trying to do. His message wasn't dangerous, but the conclusion of it means that the the army of engineers who work on MIT's weapons programs could disrupt a huge cash cow.