MIT dropped trespassing charges. (JSTOR also dropped their charges after Aaron deleted the files and promised not to do it again or something.) The feds got involved with the "hacking" because it crossed state lines, and the district attorney in Boston continued the criminal case after both JSTOR and MIT had settled with Aaron out of court.

And according to what the Aaron's lawyers have said, the prosecutors pursued the case because MIT behind the scenes wanted them to.

MIT is not necessarily blameless here. I for one will be reading that report.