It's stated in the Wired article that "much of what Swartz is accused of downloading from JSTOR is copyrighted".
It's stated in JSTOR's statement that "The downloaded content included more than 4 million articles, book reviews, and other content from our publisher partners' academic journals and other publications". (Elsewhere the size of the total JSTOR library is said to be over 6 million.)
The indictment states that downloads included "approximately 4.8 million articles, a major portion of the total archive in which JSTOR had invested. Of these, approximately 1.7 million were made available by independent publishers for purchase through JSTOR's Publisher Sales Service."
2. That Swartz intended to distribute content downloaded from JSTOR not in the public domain.
I'll grant that the absence of detail on this claim in the indictment makes it very debatable. However, it's hard to fit any explanation about his intentions to the facts as we know them without making major assumptions about information we don't have.
For instance, many people assume the downloading was for legitimate research. Not unreasonable on the face of it (given, as you say, credentials and history) but then, why does a Harvard research fellow need to covertly access JSTOR from MIT? And not just access, but download two thirds of it? There may be an entirely legitimate answer to that, but if so, it can't be gleaned from the information we currently have available.
