Yeah, this is the most likely answer. The conspiracy theories are just-so and appeal to emotion, possibly even somewhat true, but it's far more likely the DOJ has very low confidence in their case and that Boeing's excuses/answers are basically legitimate (subcontractor + airline negligence accounts for many of the serious problems).

I'd love for it to go to trial for discovery to benefit the American public, but just doesn't seem like enough of a reason to do it.