Swartz's organization seems to pretty clearly claim that both MIT and JSTOR asked the feds not to charge him. While JSTOR's statement doesn't actually say thatº, it certainly seems plausible to me since they very clearly say that they privately engaged and dealt with the matter with Swartz. You simply don't do that if you're pursuing criminal charges.

º I would probably be hesitant to say that publicly as well, considering the feds came down with a monster 35-year indictment against a juicy target. The "victim" announcing on Day 1 that they don't support the charges would not be accepted very charitably by federal prosecutors.