This is really not a failure of prosecutors. I mean it is, in the sense that they aren't actually obligated to do this, but they have every incentive to and they're human.
The real failure is of Congress not to over-criminalize minor offenses and to distinguish what these people or people like Aaron Swartz did from people doing the far more malicious things whose actions are used to justify the laws and penalties these people have been charged with.
Prosecutors, like police, have 'discretion.' The ability to decide, hey this is not that important to our community and let it go; there are more important things to do.
I read an interview with a prosecuter (it may have been an AMA on reddit) where he said that while a lot of lawyers wanted to become defence lawyers because they dreamed of saving innocent people, as prosecutor he had the power to simply drop the charges, with no reason to go to trial.
The supposed obligation of a prosecutor is to seek justice, not to put people in jail. When the incentives favor injustice, they should be adjusted; public campaigns personally shaming overzealous prosecutors are one possible disincentive that could be added.
I remember a common phrase when I was growing up: "Don't make a Federal case about it." Back then, a Federal crime was something serious, rare, and unusual. Most crime was (and still is) a local affair. Then things changed in the 80's and onward. Now double jeopardy is far too common, and trying to live your life without somehow stepping on the morass that is the US Code is difficult.
These folks meant to perform civil disobedience, to bring attention to their opinions, but to rot in jail for the rest of their lives (consider their age) is a travesty.
The real failure is of Congress not to over-criminalize minor offenses and to distinguish what these people or people like Aaron Swartz did from people doing the far more malicious things whose actions are used to justify the laws and penalties these people have been charged with.