I'll restate some of the items from your second paragraph in a way that emphasizes why I think Aaron's Guerilla[sic] Open Access[0] concept is a noble one.
He started downloading for free all the documents that were otherwise behind a pay-for-access service that placed limits on what a person could get at.
He saw that scientific research, much of which was paid for by taxes (i.e. the people), was held hostage behind a paywall and wanted to provide that information to a deserving audience.
He used various methods to circumvent attempts to prevent him from doing it.
He encountered a bug in a computer system and created a workaround.
He took measures to conceal his activity.
He behaved like many of the students on any college campus would when preparing a harmless prank or exploring a steam tunnel, and perhaps didn't want his laptop stolen.
But we can agree here. It is also my opinion that Aaron should not have been facing prison time. We have prisons overflowing with bad people that have caused far greater chaos and pain than Aaron. Aaron probably should have had a lengthy house arrest and a hefty fine. Maybe restricted use of computers, etc. And that very well might have been what he would have ended up with if he'd stuck it out.
Much of my vehemence in these discussions of the last week stems from the sheer magnitude of the onslaught that is standard practice for prosecutors. If the law and its enforcers were more reasonable in this case, I'd find it much easier to be reasonable in response. Instead, prosecutors seem to see fit to alienate a huge chunk of the population, spreading disrespect for the law (and, I guess, giving them more defendants to prosecute in the future).
I'd be perfectly happy myself, if I were Aaron, to publicly apologize, do some community service, and go on my way never to interact with JSTOR or MIT again, as this prevents the alleged harm that would have come to JSTOR with the minimum necessary imposition from the law. But I would not be happy about being bullied by prosecutors. I don't even see why house arrest should be "lengthy," or a fine "hefty," because in reality his actions had a minimal effect on MIT or JSTOR (bandwidth is cheap).
[0]http://pastebin.com/cefxMVAy