This is the definition of wire fraud:
(
http://www.law.cornell.edu/uscode/text/18/1343)
Whoever, having devised or intending to devise any scheme or artifice to defraud, or for obtaining money or property by means of false or fraudulent pretenses, representations, or promises, transmits or causes to be transmitted by means of wire, radio, or television communication in interstate or foreign commerce, any writings, signs, signals, pictures, or sounds for the purpose of executing such scheme or artifice, shall be fined under this title or imprisoned not more than 20 years, or both.
JSTOR was in a different state. Swartz caused signals to be transmitted by wire for the purpose of an artifice to defraud. The indictment is specific and cites to statutory definitions of what constitutes criminal behavior.
As I've said over and over again in relation to copyright issues, maybe things like copyright infringement should not be considered crimes at all, but right now, they are. If the elements of a crime are defined as X, Y, and Z, and there's proof that someone engaged in X, Y, and Z, then that person has committed the crime n question. Now if you want to argue that the law in question is unconstitutional for some reason, that's fine, but that's something you do at appeal. the purpose of a trial Court is simply to establish whether a certain set of facts is true or not.