I am saying that the possibility of re-offending is one of the things a prosecutor has to consider when judging the public interest, especially in a resource-constrained environment.
Had he downloaded them all individually he might have retained that right. As it stands, MIT and JSTOR both took action to remove his specific permission to do so, so it is incorrect to say that he had permission to download anything from JSTOR after his download permissions were removed.
He should be prosecuted for repeatedly gaining unauthorized access to a computer network that he had no permission to be on. The manifesto simply shows to the prosecutors why he was doing that in the first place, and why he wasn't just some bored MIT student on a pen testing spree.