I may be misconstruing what you're saying (please correct me if I am), but I don't see how MIT's and JSTOR's dismissing of the case makes them any less "primary witness material", should the authorities decide to continue prosecuting.

No you construed correctly...I think it has to do with the nature of the charges being pressed here. The feds can build a case in which there is discrete factual evidence. Either the logs show Swartz's activity or they do not. Either the computer closet was broken into or it was not. Either those documents were on Swartz's computer or they were not.

None of those facts require MIT or JSTOR to testify. A charge related to a denial-of-service, would require the cooperation of a victim...I assume...because if the "victim" isn't going to say that their network was terribly inconvenienced, then it's a hard case to prosecute.

The feds may be pursuing this hard because even if JSTOR doesn't care, there may be many people (i.e. the authors of the journal articles) who feel ripped off.