There are crimes where I think 2B1.1(b) probably makes sense (like, if you're literally stealing, or deliberately incurring monetary damage --- remember, your intent in committing a crime is extremely important, despite a common message board belief that it is somehow unknowable and a non-factor in legal decisions). But in a lot of cases, it's literally just the induction variable in a loop, and it makes no sense to boost an offense by 10 levels because you wrote "2000" in your for-loop instead of "20".
It's 2B1.1(b) that takes you from offense level 8 (0-6 months, probation eligible) to level 24 (5 years) based on 2 million dollar of incurred loss.
Again, though: the 2 million dollar figure is highly implausible. Prosecutors could have argued for it (they can argue anything they want), but it's hard to see them getting it for a non-remunerative crime that involved publishing academic journal articles.
Swartz's attorney was probably a bit rosey-eyed here, though: figure any charged computer offense probably incurs losses at least in the mid-5 figures (almost mechanically, because real companies have insurance obligations to conduct external forensic investigations when incidents like this happen), and you get to a year and change sentence pretty easily.
Actually this ran in parallel with the tail end of the Jammie Thomas-Rasset lawsuit, in which the various damage figures thrown around for sharing two albums' worth of stale, degraded-quality top-40 songs did include one in the seven-figure range.
And agree completely with your assessment of prosecutors and press releases - I told my US Attorney that I only wanted to see him on TV after a conviction. Alas, I hate defending prosecutors, but it seems completely unfair to blame her for his death.
As you suggest, my guess was that the sentence was largely going to be driven by the damages. My understanding is that the “victims” had been sufficiently browbeat into being reluctant witnesses and as you suggest, it would have just been cleanup costs.