The linked article does an OK job of documenting that contemporary news reports were too optimistic about how much Clinton's 1994 deal would constrain North Korea's bomb seeking. However, I don't think that's an adequate basis for "Clinton let North Korea get nuclear weapons" — not least because the article itself echoes, in apparent agreement, NBC's contemporary claim that NK already had a nuclear bomb.

Even setting aside that claim, I wouldn't be confident in inferring that "Clinton let North Korea get nuclear weapons" merely because Clinton made a deal and 12 years later (and 6 years after Clinton left office) NK set off a nuke. Given my original state of ignorance (I didn't know anything about this 1994 deal before this thread), I can't rule out the possibilities that (1) Clinton actually made smart moves which were later vitiated by Bush or a lower-ranked politician, or that (2) Clinton made the best of a bad hand, there being no reasonable counterfactual where a US president in 1994 could've ensured, without triggering some patently worse consequence, that NK's first nuclear explosion happened substantially after 2006.

(1/2)

I made a grab for some low-hanging knowledge on the counterfactual question by looking at the first couple of pages of a Google Scholar search for articles I could access which offered background on the topic. (I don't have the time or the interest to do anything like a real literature review, but I expect even a cursory Google Scholar search to be more reliable than a lone NewsBusters article.) Ignoring the books and paywalled Foreign Affairs articles I can't read, I got

• Michael J. Mazarr's 1995 "Going Just a Little Nuclear: Nonproliferation Lessons from North Korea" in International Security

• Larry A. Niksch's 2005 Congressional report "North Korea's Nuclear Weapons Program"

• Stephen M. Walt's 2000 "Two Cheers for Clinton's Foreign Policy" in Foreign Affairs (accessible only because Walt mirrors it on his Harvard website)

• Andrew Mack's "A Nuclear North Korea: The Choices Are Narrowing" in the summer 1994 issue of World Policy Journal

• The 1999 "Review of United States Policy Toward North Korea: Findings and Recommendations", by a "North Korea policy review team, led by Dr William J. Perry"

I haven't perused these from start to finish, and even if I had I couldn't discuss them comprehensively in a blog comment. So I have to give a radically compressed (hence necessarily selective) digest of the bits I saw which shed light on the counterfactual question.

First, Mazarr's essay. It summarizes itself, but even the summary won't fit here, so I skip to its p. 104, where Mazarr referred to NK's "alleged one or two nuclear weapons" (fitting NBC's report that NK had a nuclear weapon), and quote a longer block from the same page:

Down one road lies an ultimatum—a demand for perfect confidence and complete disarmament; its way-stations are confrontation, an end to IAEA inspections and other forms of international control [...] sanctions, and possibly war. The other road holds a more accommodating approach, lessened tensions, expanded international monitoring [...] and the hope of eventual disarmament; its price is a greater near- to medium-term risk that the proliferant might be able to hide a rudimentary nuclear program.

Mazarr adds that, in practice, the US "always resorts" to the softer approach "in cases of hard-core proliferation", having "accepted ambiguous proliferation in India and Israel for many years", and likewise didn't pursue an all-out approach against India & Pakistan. Further along, on p. 110, in the section on sanctions:

Even had a tougher approach been more appealing, there was little chance it would have worked. North Korea had a long history of rejecting international opinion when phrased as a demand and accompanied by sanctions or the threat of them. Nor could economic sanctions have been effective without the participation of China, South Korea, Russia, and Japan, each of which expressed some degree of unease with a confrontational approach to the North, and reluctance to take any steps that might spark a rapid collapse of the North Korean system.

The section on sanctions was generally pessimistic, though Mazarr granted that "the de facto sanction of existing trade restrictions" could help shape "a proliferant's motives" (p. 111), and that NK seemed to have an interest "in avoiding condemnation and sanctions as voted by the Security Council" (p. 112). Mazarr was even more doubtful that military action would "have offered a definitive answer to the North Korean nuclear challenge" because it could have "led directly to a Korean war" and "military strikes [...] probably would not work" anyway (p. 113).

Mazarr's essay was most optimistic about the kind of approach represented by Clinton's '94 agreement: "a broad-based policy of incentives built around the offer of a package deal" (p. 114). Even a rejected package deal "would have its uses" because it "would force North Korea to make a clear choice, deprive it of excuses, and seize the political high ground, firming up a political consensus (including China) for UN sanctions" (p. 117).

Niksch's report doesn't seem useful for the counterfactual question at issue, because the report is mainly about the (second) Bush administration's goals & actions. My skimming revealed a description of the US's obligations under the '94 Agreed Framework, but no substantial, explicit evaluation of alternatives to the Framework.

Walt's article is a general assessment of Clinton's foreign policy. From its paragraph about the 1994 NK deal, on pages 72-73:

Hard-liners have criticized Clinton for rewarding North Korea's defiance of the nonproliferation regime, but they have yet to offer an alternate policy that would have achieved as much with as little. A preemptive air strike might well not eliminate North Korea's nuclear capability. Moreover, both South Korea and Japan opposed the use of force. [...] the situation called for flexibility, persistence and creativity; the administration displayed them all. Without the 1994 Agreed Framework, North Korea would almost certainly have obtained enough fissile material for a sizable number of nuclear bombs. [...] Given the limited array of options and the potential for disaster, Clinton's handling of North Korea is an impressive diplomatic achievement.

Mack's essay reminds me of Mazarr's in its scepticism about sanctions (e.g. p. 32: "What all this suggests is that imposing sanctions will be far more problematic than their more naive proponents in the West realize"), and Mack was at least as negative as Mazarr about military action, writing on p. 33 that "[t]he idea of resolving the nuclear issue by 'taking out' the Yongbyon nuclear facilities suffers from three fatal defects". Those three, briefly: (1) "it is by definition impossible to hit unknown targets" potentially kept secret by a "paranoid" regime; (2) "'surgical strikes' against Yongbyon might not only fail to destroy all of the North's nuclear program, they would also unleash a very unsurgical war against the South"; and (3) "it would be politically impossible to pursue the military option until the less risky alternatives of persuasion and sanctions had [...] failed. But sanctions would likely take years to have the desired effect". Ultimately, Mack was not sure anything would work. From p. 35:

Given the very real possibility that neither persuasion nor bribery, economic coercion, military action, or even unilateral reassurance will divert Pyongyang from its nuclear path, the international community needs to start thinking about what this may mean for regional—and global—security.

The 1999 Perry et al. review reads to me as broadly positive about the Agreed Framework, asserting on p.2 that it

succeeded in verifiably freezing North Korean plutonium production at Yongbyon — it stopped plutonium production at that facility so that North Korea currently has at most a small amount of fissile material it may have secreted away from operations prior to 1994; without the Agreed Framework, North Korea could have produced enough additional plutonium by now for a significant number of nuclear weapons.

The review team behind the report recommended on p. 6 that the Agreed Framework "be preserved and implemented" as one recommendation of six:

With the Agreed Framework, the DPRK's ability to produce plutonium at Yongbyon is verifiably frozen. Withou the Agreed Framework, however, it is estimated that the North could reprocess enough plutonium to produce a significant number of nuclear weapons per year. The Agreed Framework's limitations, such as the fact that it does not verifiably freeze all nuclear weapons-related activities [...] are best addressed by supplementing rather than replacing the Agreed Framework.

Insofar as these sources are accurate and I've understood and digested them properly, it's not only possible but likely that Clinton did about as well on this count as a different president could've. If so, then (even if NK didn't already have a nuclear weapon in '94) I'd think it unfair to assert that "Clinton let North Korea get nuclear weapons" as if there were an alternative decision Clinton could've taken to delay North Korea's first nuclear test for 13+ years.

(2/2)

The argument here seems to be: North Korea built nuclear weapons, the 1994 treaty was supposed to prevent that, therefore let's blame the guy who was President in 1994 for North Korea building nuclear weapons.

Similar reasoning could just as easily place the blame on the Reagan administration.

Unless I'm missing something, and there is some reason why that 1994 treaty left the US in a hopeless position in 2002, unable to intervene while North Korea kicked out IAEA inspectors, unsealed its fuel rods, and built nuclear weapons.