"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.