To be fair, isn't that how criminal law generally works? Once you report a crime (or the authorities find out somehow), can't you still be prosecuted even if the victims say it's "no big deal"?
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.
Unfortunately for Swartz, he is neither - on the contrary, he's been constantly and loudly criticizing the government, so he gets the "by the book" treatment to its worst possible conclusion.