Swartz's prosecution alleges --- credibly, given what Swartz allegedly posted prior to scraping JSTOR --- that Swartz intention was to liberate data from a commercial database onto file sharing networks, making intent a much easier case to prove. Moreover, the indictment is at pains to point out that MIT and JSTOR repeatedly attempted to stop Swartz from continuing his plan, and found themselves in a cat-and-mouse game with Swartz eventually trespassing to maintain access.

PadMapper found itself having exceeded Craigslist's terms, found out by having its access withdrawn and becoming the target of a civil suit, and did not (directly, at least) attempt to evade the countermeasures Craiglist applied to prevent them from obtaining further access.

Whether or not you believe Swartz did something wrong here (I do) or whether you think he should get a felony conviction for doing it (he probably shouldn't), you can see pretty clearly how JSTOR had no straightforward civil remedy to what Swartz was doing. Swartz was playing chicken with them, and he lost --- or rather, his bicycle collided with JSTOR's semi truck at high speed.