The spate of new NSA disclosures substantially raises the stakes of this debate. We now know that the intelligence establishment systematically undermines oversight by lying to both Congress and the courts. We know that the NSA infiltrates internet standard-setting processes to security protocols that make surveillance harder. We know that the NSA uses persuasion, subterfuge, and legal coercion to distort software and hardware product design by commercial companies.

We have learned that in pursuit of its bureaucratic mission to obtain signals intelligence in a pervasively networked world, the NSA has mounted a systematic campaign against the foundations of American power: constitutional checks and balances, technological leadership, and market entrepreneurship. The NSA scandal is no longer about privacy, or a particular violation of constitutional or legislative obligations. The American body politic is suffering a severe case of auto-immune disease: our defense system is attacking other critical systems of our body.

First, the lying. The National Intelligence University, based in Washington, DC, offers a certificate program called the denial and deception advanced studies program. That's not a farcical sci-fi dystopia; it's a real program about countering denial and deception by other countries. The repeated misrepresentations suggest that the intelligence establishment has come to see its civilian bosses as adversaries to be managed through denial and deception.

We learned months ago that the Director of National Intelligence James Clapper lied under oath to Congress. Now, we know that General Keith Alexander filed a "declaration" (which is like testifying in writing), asserting an interpretation of violations that the court said "strains credulity". The newly-disclosed 2009 opinion includes a whole section entitled "Misrepresentations to the Court", which begins with the sentence:

The government has compounded its noncompliance with the court's orders by repeatedly submitting inaccurate descriptions of the alert list process to the FISC.

General Alexander's claim that the NSA's vast numbers of violations were the consequences of error and incompetence receive derisive attention. But this claim itself was in a court submission intended to exculpate the agency from what would otherwise have been an intentional violation of the court's order. There is absolutely no reason to believe the claims of incompetence and honest error; there is more reason to assume that these are intended to cover up a worse truth: intentional violations.

Second, the subversion. Last week, we learned that the NSA's strategy to enhance its surveillance capabilities was to weaken internet security in general. The NSA infiltrated the social-professional standard-setting organizations on which the whole internet relies, from National Institute of Standards and Technology to the Internet Engineering Task Force itself, the very institutional foundation of the internet, to weaken the security standards. Moreover, the NSA combined persuasion and legal coercion to compromise the commercial systems and standards that offer the most basic security systems on which the entire internet runs. The NSA undermined the security of the SSL standard critical to online banking and shopping, VPN products central to secure corporate, research, and healthcare provider networks, and basic email utilities.

Serious people with grave expressions will argue that if we do not ruthlessly expand our intelligence capabilities, we will suffer terrorism and defeat. Whatever minor tweaks may be necessary, the argument goes, the core of the operation is absolutely necessary and people will die if we falter. But the question remains: how much of what we have is really necessary and effective, and how much is bureaucratic bloat resulting in the all-to-familiar dynamics of organizational self-aggrandizement and expansionism?

The "serious people" are appealing to our faith that national security is critical, in order to demand that we accept the particular organization of the Intelligence Church. Demand for blind faith adherence is unacceptable.

What did we actually know about what we got in exchange for undermining internet security, technology markets, internet social capital, and the American constitutional order? The intelligence establishment grew by billions of dollars; thousands of employees; and power within the executive. And we the people? Not so much. Court documents released this week show that after its first three years of operation, the best the intelligence establishment could show the judge overseeing the program was that it had led to opening "three new preliminary investigations". This showing, noted Judge Walton in his opinion, "does not seem very significant".

If this was the best the intelligence community could put on the table when it faced the risk of judicial sanction, we can assume that all the hand-waving without hard, observable, testable facts is magician's patter, aimed to protect the fruits of a decade's worth of bureaucratic expansionism. Claims that secrecy prevents the priesthood from presenting such testable proof appeal to a doctrine of occult infallibility that we cannot afford to accept.

In August, 205 members of the House voted in favor of the Amash-Conyers Amendment that would have rewritten Section 215 of the Patriot Act, the section used to justify bulk collection of domestic phone call metadata. At the time, this was a critically important move that was highly targeted at a narrow and specific abuse. But the breadth and depth of organizational deception and subversion force us to recognize that we need reconstruction that goes much deeper than any specific legislative fix.

We need a fundamental organizational reform. The so-called "outside independent experts" committee which the president has appointed, with insiders' insiders like Michael Morell and Richard Clarke, will not come close to doing the trick. Nor is it likely to allay anyone's fears who is not already an Intelligence Church adherent.

Given the persistent lying and strategic errors of judgment that this week's revelations disclosed, the NSA needs to be put into receivership. Insiders, beginning at the very top, need to be removed and excluded from the restructuring process. Their expertise led to this mess, and would be a hindrance, not a help, in cleaning it up. We need a forceful, truly independent outsider, with strong, direct congressional support, who would recruit former insider-dissenters like Thomas Drake or William Binney to reveal where the bodies are buried.

Anything short of root-and-branch reconstruction will be serving weak tea to a patient with a debilitating auto-immune disease.

• The spelling of Richard Clarke's name was amended at 9.30am (ET) on 13 September 2013