One of the major questions about Aaron Scwartz's suicide has been the role of MIT. Kevin Cullin at the Boston Globe (paywall) answers that one. One of Swartz's earlier lawyers (there appear to have been at least three) had negotiated a plea bargain which was basically a pledge not to do crap which if broken would have resulted in jail time. When the prosecutors asked MIT to approve they said no. Hal Abelson's investigation may take a few heads on this one.
The overcharging was certainly a bargaining chip that the AUSA Steve Haymann shoved across the board. What was the real threat. Probably Swartz saw that one of the conditions of parole after serving a short time would be not being allowed to touch a computer for many, many years. That indeed was a death threat to someone who lived on line.