Because they didn't know what was going on and needed help to figure it out. It's all laid out in the Abelson report.
If you're looking for a key juncture at which MIT made a mistake, I would ask why they didn't make a statement similar to the one JSTOR made after the civil settlement: basically saying "we're satisfied that this is resolved and don't have any interest in further legal actions being taken". (I'm not sure this would actually have stopped the prosecutors, since they seemed bound and determined to "get" Swartz no matter what, but at least it would have been something.)
This is common knowledge about the case, also found in Wikipedia: http://en.wikipedia.org/wiki/Aaron_Swartz#JSTOR
http://www.mass.gov/courts/courtsandjudges/courts/districtco...
See, the problem here is that we are talking about giving aid to overly aggressive prosecutors, whose entire careers are devoted to undermining civil rights and destroying their targets. If that is the sort of prosecution you are aiding, yes, you should share in the blame for what happens to the prosecutor's victims.