The important difference here is that the DoJ made that argument before a court and didn't decide for itself in a "dark, windowless room". You're invoking an image of unfettered power that doesn't match reality. This was a law suit, by definition it was going to be settled by the judiciary, not the DoJ.
I think the chilling thing is that, right or wrong, many people believe the JD thinks it ought to have those kinds of powers. Any move it shows that looks like they are trying to actually grab it ("You aren't allowed to contest an NSL that way.") makes people uncomfortable.
I do agree that the system, so far, is working as designed, and it is just appearances that are causing discomfort.
