The FAA has a tendency to punish deliberate acts or serious lack of judgement, i.e. "I'll fly under this bridge, it'll be awesome."

When mistakes happen by accident, they tend to give people lots of slack to encourage honest accounts so that they and the rest of the community can learn from the mistake. This is the reason behind things like the NASA form, which is sometimes seen as a "get out of jail free" card. You write a detailed account of what happened after certain kinds of accidents/incidents, and if they conclude that you weren't being too stupid, or it wasn't a repeat issue that you should have learned from, they'll skip certain minor enforcement actions against you.

Because pilots are humans, and humans make these types of human-mistakes generally. If your safety protocol relies on humans being perfect, you better resign yourself to a decent number of crashes. Better to build a system where openness around unintentional mistakes is encouraged, and then design that system to be redundant even in the face of human error.

I agree, but in this case the automatic systems to avoid human error were the primary systems, and the humans knew they were malfunctioning before takeoff, and yet failed to double check for human error and flew the flight despite it being illegal to do so with the automated system malfunctioning. So yes you want to design your system to limit the impact of human error, but the human pilots also bear a very large responsibility too. Not as much as the airline for sure, but I could see why the initial verdict would lean toward negligence from the sheer number of lapses in judgement that were made.