Exactly - and such legislative overreach is often rebuked and/or set aside by the courts. But legislation is not required to be pre-certified as Constitutional before it is passed by Congress or signed by the President. This is probably a good thing, because otherwise it would be much more difficult to bring challenges on unforeseen grounds that manifested after the legislation had gone into force, and you'd have a legislative dictatorship.
As for the DoJ, my understanding is that as an executive branch agency it has the obligation to make the most of its power to execute the laws on behalf of Congress. The amount of discretion available to the Attorney-General varies from law to law; the executive can't just abdicate its own power.
Now, the Obama administration has filed briefs arguing that the Defense of Marriage Act is unconstitutional for the upcoming case in the Supreme Court. Isn't that the exact opposite of what I'm saying above, you might ask? My answer to that would be no, because in the meantime it is still implementing DOMA; for example, by forbidding gay couples to file taxes as a married couple even if they married under state law. If I were married to a partner of the same sex, and we filed a joint tax return, the IRS would write back and say 'you can't do that.' If I then sued the government, they would be obliged to defend the suit and stand up for DOMA until such time as the Supreme Court overturns it (if they ever do). The administration's brief to the Supreme is a non-binding policy suggestion about how the constitution should be interpreted, which the Justices may choose to ignore. The administration's brief in my hypothetical lawsuit against them would be arguing for the application of the law as it currently stands, not as the administration might wish it to be.
Even soldiers (with guns, while under fire) are expected to act legally, and ethically where those standards differ, and we need to hold everyone - public servant or not, to the same standard.
Not only does such a law (making challenging a gag a crime) clearly require authority the people would not and did not grant to the government, but applying such a law to stifle oversight of your actions is criminal - especially when in a sensitive position over so many.
The thing is it takes time to establish exactly what the right standards are, and it's not necessarily settled after today; there might be a circuit split or appeals to confuse the issue in the coming years. Where national security is concerned, the standards are different from those we're familiar with in criminal cases, for example in not requiring a warrant for issuance. See https://en.wikipedia.org/wiki/National_security_letter
Now, you say that these require authority that the people 'would not and did not grant to the government.' I'd agree that they should not, but as I recall there was quite a lot of popular support for the PATRIOT act when it first passed, and the concerns of civil libertarians (including mine) were pretty much sidelined.
No, the time being used to establish the right standard was being spent in Plato's day. Now we know that this is a bad way to act, AND a bad way to run a country. You can never let the watcher watch themselves. Any attempts must be punished as heavily the crimes they could start to cover up.
I go further in saying that these are powers people COULD NOT grant to government. Our legal philosophy (not just current laws) hold that there are things we cannot "agree" to - to be killed for instance, and we can't agree to something on someone else's behalf except in very limited circumstances, and until they are available to confirm those decisions themselves.
Using a NSL letter to gag an otherwise legitimate court proceeding for a period of time wouldn't remove the checks and balances of society - but making seeking redress in court illegal altogether, does. And it effectively makes us slaves - having no power to control or petition our government. As above, we couldn't agree to that.
As for support for the patriot act, 1) Bush knowingly lied about the perpetrators and circumstances of the 9/11 attacks, and the potential remedies. If this was a civilian action he'd be known as a criminal. Many people were convinced by his lies, but ultimately it was pushed through regardless of popular support. 2) It doesn't matter because you can't agree to take someone else's rights away and any government that pretends you can isn't a legitimate representative of any people.
After all, we (The citizens of UN signatories) wouldn't let India end its current "rape crisis" by simply removing women's rights to complain about being raped.
As for the DoJ, my understanding is that as an executive branch agency it has the obligation to make the most of its power to execute the laws on behalf of Congress. The amount of discretion available to the Attorney-General varies from law to law; the executive can't just abdicate its own power.
Now, the Obama administration has filed briefs arguing that the Defense of Marriage Act is unconstitutional for the upcoming case in the Supreme Court. Isn't that the exact opposite of what I'm saying above, you might ask? My answer to that would be no, because in the meantime it is still implementing DOMA; for example, by forbidding gay couples to file taxes as a married couple even if they married under state law. If I were married to a partner of the same sex, and we filed a joint tax return, the IRS would write back and say 'you can't do that.' If I then sued the government, they would be obliged to defend the suit and stand up for DOMA until such time as the Supreme Court overturns it (if they ever do). The administration's brief to the Supreme is a non-binding policy suggestion about how the constitution should be interpreted, which the Justices may choose to ignore. The administration's brief in my hypothetical lawsuit against them would be arguing for the application of the law as it currently stands, not as the administration might wish it to be.