I think that the central assumption of your post is that I'm making the assumption that there was a systematic conspiracy to bring him to ruin. I am not alleging that. Neither am I stating anything towards the question whether or not his actions ran afoul of the spirit of the law. (indeed as this man asserts, there is reason to question that as well) I am simply stating an observation based upon the following;
a) the prosecutor's office has limited, finite resources to pursue cases
b) The prosecutor has discretion over the choice of cases
c) The office is judged by its record when it comes to the number of convictions and the quality of the cases pursued
d) It is reasonable to assume that the prosecutor acts as an agent, pursuing their own agenda versus the spirit of their duties. (the principal agent problem)
e) The legalities in Aaron's case are complicated and understood by a few.
f) It is also reasonable to assume that the case is inherently more risky than an open and shut guilty conviction, due to various factors such as, 1) the desire of MIT, JSTOR not to prosecute themselves, 2) expert witnesses such as the author of the article willing to provide testimony against the case, 3) the lack of a direct victim, and 4) questions over the inherent legality of the action itself.
g) In the above context it is reasonable to assert that the prosecutor without their well established tricks may have indeed lost this one if Aaron had the resources to have his day in court.
h) Aaron has a demonstrated previous track record of acting against the interests of the US govt. and the individuals it consists of.
i) Those individuals within the government have a social network
j) The said individuals are capable of and are willing to influence one another through this network
k) The prosecutor is a part of such a network by her very position within the government.
It is therefore reasonable to assume from the above assertions that it is likely the prosecutor was influenced to pursue the case with more rigour than necessary.