Choosing between serving more time and serving less time isn't much of a deal when you think what you did was right and you are innocent.
Doing what you think is right when you know it is probably illegal is called civil disobedience, and it usually entails a willingness to go to prison when done right.
Why does it matter what the defendant thinks is right?
But in no other country are the chips stacked as high as they are against the defendants as they are in the U.S. in a federal case. Ortiz, via her office, charged Aaron with 11 counts of fraud. If you think you're innocent, there's no negotiating out of pleading guilty to at least some of the charges. That is fundamentally wrong.
I don't think plea bargaining is the best way to run a justice system either, but that's the reason why.
About as much as putting a gun to one's head is a form of negotiation.
"While at the same time, his defense counsel would have been free to recommend a sentence of probation. Ultimately, any sentence imposed would have been up to the judge."
This was not negotiation with a gun.
Swartz was first to point a gun (i.e., initiate force). No one forced him to keep breaking into MIT's wireless networks and its wiring closet, nor did anyone force him to violate JSTOR's rules and copyrights. He chose to do all of those things, and the government was merely doing what it's supposed to do: retaliate.