Right. Plea deals are "I'll plead guilty and save you the trial in exchange for this sentence."
Depending on the court, plea deals can be a horrible gamble by a defendant. Generally you have to enter your guilty plea first, and then the judge decides if they want to let you have that sweet, sweet sentence the prosecution offered.
I know someone who went to court having been offered a plea deal for probation and got 80 years instead when the judge rejected it and sentenced them.
Yeah, this shocked me when I learned it. The actual "deal" is the defendant agrees to plea guilty in exchange for the prosecution giving a specific recommendation of sentence. (In most cases, there are some exceptions of course)
Boeing isn't pleading guilty on its own - it's also agreed to damages.
I agree that a defendant pleading guilty on their own (and throwing themselves on the mercy of the court) would be hard to reject. That isn't what's happened here - the prosecution has, presumably, agreed to the damages, so this is a plea deal, right?
Without turning this into a criminal procedures lecture, the practical difference surrounds who decides the punishment. When a judge rejects a deal they are asserting control over punishment. But a prosecutor can fight back by dropping charges, or reducing to lesser-but-included charges [insert lecture re elements] which would place a cap on the max punishment the judge could adopt. It is a back-and-forth fight between the prosecutor and the judge about who decides punishment, who represents the wishes of the people.