Sorry but it is your "re-contextualizing" that is ridiculous.
Swartz never engaged in violence or threats of it. All he did was to download a large number of publicly funded scientific papers that he should have had access to anyway. MIT did not just report him. They made sure that the secret service was there in a couple of minutes and then they insisted on prosecuting him. One could argue that it was the MIT's insistence on prosecution that did him in, as much as the eagerness of the DoJ.
MIT made a number of bad decisions and this latest one only continues this trend. Until someone is named to take personal responsibility for those decisions, or someone does the decent thing and owns up to them, the responsibility must lie with MIT as an institution.