What you're saying about MIT's network policies doesn't even help your point, it helps mine, unless you actually believe that e.g. running BitTorrent on MIT's network should justify really stiff penalties just because of some DoD involvement in other parts of MIT's network.
By the way, one of our clients has been on-and-off-again funded by the DoD, and we are directly responsible for their network, and we were audited by representatives of the army not too long ago. So, I do have some notion of the expectations for network security in such an environment, and I can tell you that everyone that matters there -- including the Army -- would think I was insane if I suggested that the unauthorized use of the network there to download paywall'd scientific journals should be a felony offense, or one that should result in any jail time at all.
Whether or not MIT's status as a defense contractor "colors" other people's decisions or not is irrelevant. What has been under discussion is whether or not those decisions were reasonable and proportionate to the crime committed, and you are doing absolutely nothing to argue that point.
Your profile claims that you are both a lawyer and an engineer, but bewilderingly, you don't seem to be accounting at all for what Swartz was actually doing. You seem to be making an argument that, because there were sensitive portions of MIT's network, even though it was established that Swartz was not accessing or attempting to access those portions, it's somehow justifiable to punish him as though he were. If that is your argument, I think you ought to reconsider that condescending tone on your last line.
If your point is that any unauthorized access, either of facilities or network closets, at MIT should be prosecuted more heavily merely because of MIT's DoD involvement, then let me again circle back to my point, which is that such policies are completely at odds with the ideals that made MIT an attractive talent pool for the DoD in the first place.