I took these to be part of the DOJ:

"The criminal investigation and today’s indictment of Mr. Swartz has been directed by the United States Attorney’s Office. It was the government’s decision whether to prosecute, not JSTOR’s. As noted previously, our interest was in securing the content. Once this was achieved, we had no interest in this becoming an ongoing legal matter."

So it's not as if anybody outside the government was still pressing charges over this.

Judges, United States Attorneys, they could have all put a stop to this, instead they allowed it to roll on destroying a life in the process, regardless of what Aaron did to himself or not.

A prosecutor's duty and role is to seek justice[0]. Justice isn't always black and white, but it certainly isn't applying the toughest charges that could possibly be made to stick nor seeking the highest possible penalty in every case. The prosecutor should attempt to determine what a just outcome to a case would be, then seek to achieve it.

[0] http://www.americanbar.org/publications/criminal_justice_sec...

I would agree with you if the separation of powers would work flawlessly, but it seems to me that even in many modern democracies, prosecutors have the means to do things that are quite punishing.