JSTOR is being very vague about their role in this, so that might unfortunately be wrong about just how settled JSTOR considers things on their side. Their statement feels extremely carefully worded: http://about.jstor.org/news-events/news/jstor-statement-misu...
MIT (and the alleged disruption to other MIT JSTOR users' access) may also be relevant to the decision to charge.
My understanding is that MIT has a freewheeling attitude to information, but also deep organizational and funding links to national security institutions. So their hacker ethos might tell them to brush it off, while their federal relationships require them to take a tougher stance.
In terms of broader implications, I would actually have many fewer problems with MIT pressing straightforward trespassing charges. If he broke into a server room and messed with equipment there without the owner's permission, they could prosecute that under very ordinary state criminal law long predating the computer age.
It's the weird "stealing documents from JSTOR" federal case under the Computer Fraud and Abuse Act that's more worrying, because it's extremely vague what those kinds of charges can cover (in some interpretations, essentially any violation of a ToS).
