The way I see it, I think someone else already mentioned it, is that Sony made a lot of promises about the PS3 that they later went back on. They advertise it as doing pretty much everything when the truth is that there's a lot it can't do (like be affordable to the working poor, which a lot of Americans are whether they know it or not, although that's less of an issue with lowered prices)... My point is that Sony stated their console would be made a certain way, then they went back on their word later on and changed it.
Now I don't know if it was talked about BEFORE or AFTER the console came out (the changing of the OS option), but if it came out afterwards, than yeah the USAF has something to be pissed off about. It's not that they can't just do it themselves (and may well be doing so already), it is more about the fact that you can't just start changing things willy-nilly and expect to get away with it. Sales, profits, popularity... for a company like Sony (and Nintendo) it is a very important thing.
It also points towards Sony trying to find ways to keep the hackers at bay when I've said before they should just stop trying, it's not going to happen. The Wii's been cracked since almost day one, and I know that people have done interesting things with the Xbox and possibly the 360, as well.