Activism, or hacktivism, is one thing. Breaking critical research tools for millions of customers worldwide is abuse, and clearly criminal in several ways. I'm afraid that Aaron earned prosecution. The extent of the prosecution seems severe, but as best I can tell, the prosecutors were quite willing to "deal" for a a very low sentence, as long as the deal included a felony conviction. I'm afraid that that haggling over the charges and the sentence is _normal_ for prosecutors.
One thing I learned from Wikipedia that I hadn't heard anywhere else is that, a few years earlier, Swartz first downloaded the Library of Congress's "complete bibliographic data set" (whatever that is), then a bit later downloaded millions of public domain court documents from a paywalled system called PACER. The Library of Congress normally charged fees to access the former, and the latter charged users 8 cents per page back then (now it is 10 cents per page up to $3 per document). Despite gaining the attention of the FBI, he didn't get so much as a slap on the wrist for either one.
So we have a couple aspects potentially contributing to what happened. First, Swartz probably felt reassured by his past experiences that, even if caught, he wouldn't get in trouble. Second, he didn't make any friends in the government by pulling his first two stunts, so when federal prosecutors realized they could get him, they went overboard. This is just conjecture, of course, but I wouldn't be surprised if it was true.