Realized today that I'd meant to come back to this topic and never did. Hope no one minds me bringing the thread back from the dead again.
Batman is a response to the failures of the state, not to its normal functioning.
And Jack Bauer is not?
No, he is an agent of the state who operates when the state is functional. If the state has become so fundamentally dysfunctional that it has violated the social contract, as the Gotham City government did, then Bauer ought to launch a revolution and overthrow the United States government, not continue working for it.
And while we're at it...how does one know that Section 31 is not?
There is no evidence that Section 31 is an agency that formed in response to the United Earth government breaking the social contract. All the evidence suggests that it originated as a secret cabal of United Earth Starfleet (UESF) officers who decided to interpret a provision of the UESF Charter that called for leniency for officers who violate UESF regulations in times of crisis as somehow authorizing a permanent organization with eternal carte blanche to disregard the law at all times.
Remember, Enterprise showed that, in the beginning, Section 31 was a lot less "iffy". One might, therefore, conjecture that as the decades went by, and as the UFP government became more and more weak and naive, The Bureau realized that they had to do the work that the government was not willing to do, in order to defend the UFP.
But there's no evidence of that; that may be what Section 31 tells itself to justify its actions, just as the Gestapo used to claim that it
had to torture anti-Nazi resistance fighters because they were terrorists who were outside the protection of international law, but this does not make it true.
In particular, I would point out that there is not a single Section 31 operation we have seen canonically that has
not spectacularly backfired on them due to
their naiveté. In "Affliction"/"Divergence," they made a deal to let the Klingon Defense Force kidnap Doctor Phlox from Earth so as to cure the Augment virus and stabilize the Klingon Empire, only to find themselves double-crossed by the Klingons who then attacked
Enterprise and
Columbia and were ready to murder Phlox and their own colony.
In "Inquisition," they tried to recruit Dr. Bashir by subjecting him to psychological torture, only to have him turn on them.
In "
Inter Arma Enim Silent Leges," they framed for treason a pro-Federation alliance, pro-diplomacy Romulan Senator so as to put the Chairman of the Tal Shiar onto the Romulan Continuing Committee -- they actually
trusted that the
head of the Romulan secret police was honestly working for them and not working as a triple agent. Since NEM established that the Federation-Romulan alliance splintered after the war and that the Tal Shiar did not stop the assassination of the entire Romulan Senate by Shinzon and his anti-Federation military backers, we know that Chairman Koval either betrayed Section 31 or failed them utterly.
And in the DS9 Final Chapter arc, we discover that Section 31's campaign to commit genocide against the Founders has only left the Female Shapeshifter so bitter and with nothing to lose that she was willing to force a pyrrhic victory on the Allies rather than just surrender as she would have been inclined to do had her race not been facing extinction -- and as she did once she knew her race would survive.
Meanwhile, if we expand our plate to include the novels, Section 31 displays even
more gross incompetence.
In
DS9: Abyss, they arrange for the massacre of a Federation colony by the Dominion -- committing treason in the process, by the way -- in order to manipulate a genetically enhanced Human into joining the bureau, only to watch as Dr. Locken then turns on them and tries to set himself up as head of a specially-bred Jem'Hadar army (forcing them to rely on Bashir and the DS9 crew to stop him).
We also discover in that book that Admiral Dougherty's incredibly ill-thought-out alliance with the backstabbing Son'a in INS was a Section 31 operation.
In
Section 31: Cloak, we discover that Section 31 was behind the research into the Omega Molecule that ended with the subspace explosion that permanently ended warp travel in the Lantaru Sector.
In
Section 31: Rogue, we learn that Section 31 traded away control of an area of space containing a singularity that could have been a source of unrivaled power -- or of the end of the known galaxy -- in exchange for an outdated list of out-of-favor Tal Shiar operatives in Federation space.
In
TOS: The Case of the Colonist's Corpse, we discover that Section 31 spied on Sam Cogley on suspicion of treason because he was too much of an individualist... and then lost their agent assigned to him when he quit the organization and went to work for Cogley.
In
TNG: A Time to Kill, Section 31 stands around doing nothing to stop the crimes being committed by Federation President Min Zife as he's committing them... except preparing to commit genocide against the Tezwan people by blowing their world up. In
A Time to Heal, they then intervene after Starfleet has forced Zife out of office by
secretly assassinating... and then, as established in
Articles of the Federation, do nothing to cover up Zife's death (no holograms, no agents surgically altered to look like him, nothing), thus ensuring that eventually the assassination will get out when someone realizes that no one's seen the former President since his resignation.
And in the ENT Relaunch, their brilliant idea for infiltrating the Romulan Star Empire is to send Trip, an
engineer, into Romulan space... whose partner is promptly killed and whose cover is promptly blown by the Romulan government.
All the while, Section 31 has consistently and spectacularly failed to predict or defend against major threats to the Federation, including Gul Dukat's Dominion coup on Cardassia, the rise of Shinzon and the Senate's assassination, Klingon infiltration of the Federation government in the 2260s, Dominion manipulation of the Klingon government, and the rise of the Maquis.
They've been shown as doing one truly competent thing that didn't backfire on them: Giving the codes to the Verteron Array to the NX-01 crew in "Terra Prime." That's it.
But why not just use SI, or Federation Security? Simple: These organizations have rules--rules which they cannot bend. These rules thus tie the hands of the Federation, inviting it to attacks by those who know its limits, and seek to exploit them.
So long as a government follows an intrinsic standard of law, this kind of injustice will continue to harm the Federation. (Note: Picard brought this up in "Justice": "There can be no justice, so long as laws are absolute!", to which Riker agreed, "Since when has justice been as simple as a book?")
There's a big difference between recognizing that justice requires some room for individual judgment -- which is the role of a judge in the judicial system -- and deciding that the ends inherently justify the means and that the rule of law and sentient rights should not stop the government from doing whatever it wants in service of the false god of national security.
With the nationalization of Section 31, this organization can thus become what it was supposed to be--a group which is allowed to bend certain rules during a crisis (when SI and FS could not act, due to rules),
Starfleet bends certain rules during crises all the time.
These instances would be the sole discretion of the president,
The sole discretion of the President?
Really? How does that preserve the rule of law? Why should the President be allowed to order someone to break the law whenever he wants so long as he uses the magic words "national security?" How is that not the establishment of an undemocratic threat to Federation liberty?
And...in order to
ensure that Section 31 would not go in over the President's head, he/she could assign members of the Kirk Cabal (imagine that!

) to
report on The Bureau's actions,
without interfering
unless so directed by the President.
Or maybe we can just abolish Section 31 and use Starfleet and Federation Security, since it's been established time and again that Section 31 are not only criminals, but incompetents to boot.
BTW...there is precedent in Star Trek for "compromising values" for the sake of saving lives, and doing what is right.
Sure. But Section 31 does not do what is right.
Consider: In "Extreme Measures" Bashir was willing to do whatever was necessary to save Odo. He was willing to falsify information about a cure in order to lure Section 31 to DS9.
Not necessarily illegal. Law enforcement officers are allowed to lie in order to apprehend a criminal.
He was willing to capture and shoot an unarmed man--Sloan.
An unarmed man who had on numerous occasions already demonstrated his ability to pose a severe threat to others' safety even without arms.
He was willing to retain Sloan without a warrant--unless you want to count Sisko's sanction an "unofficial" warrant.
Even civil libertarians believe that there is a such thing as probable cause; Bashir had more than enough probable cause to arrest Sloan.
He was willing to use Romulan Mind Probes to glean the info from Sloan's mind--
And for that he should have been charged and tried by a court-martial, especially since there is no reason to think that legal methods of interrogation would not have functioned and since it was apparent that they had at least several weeks left to stop the Founder virus before it would kill the Great Link.
Bashir...was...willing...to...torture him!
And he was wrong to do so. Section 31 managed to corrupt him even without his joining them.