This is the most technically competent charging document I've ever read. I guess there must have been some hackers on the grand jury.
Paragraph 35 & 36: which "protected computer" on MIT's network did he access? Certainly they're not trying to claim his laptop was a protected computer? Are they talking about the DHCP server or whatever registration frontend MIT has for the DHCP assignments? I have trouble with the concept that a violation of a computer use agreement (when there are no operative security barriers in place) constitutes a violation of the computer fraud and abuse act. Then again, I've always thought that act was vague and therefore overbroad.
Obviously what he did was bad in some sense (at least from the perspective of JSTOR and MIT), but even if it should be a crime rather than a civil dispute or internal disciplinary action at MIT, I don't like the fact that just about any misbehavior on the internet becomes a federal case because the probability of no interstate resources being used is very low.
Finally, I take issue with the notion that someone who is accessing a service through a public interface is criminally responsible for downtime if too high an access rate causes service degradation or an outage. The claims that JSTOR's servers were overloaded and (one?) even went down at some point are clearly there to set up a later claim of damages. Haven't they heard of rate limiting (in this case, since it was a rogue laptop stashed in a data closet, rate limiting by IP)? That wouldn't work against a concerted denial of service attack, but this was no denial of service attack. JSTOR seems to have been relying on manual intervention to stop article leeching that could lead to a (partial) outage. That's naive, and not a good idea.