That is one of the worst articles I've ever read on Iran. The writer has no grasp of the technical nature of the IAEA or safeguards, how power reactors work or the Russian offer of assistance.
Comparing it to Kim Jong Ill makes no sense, as when the IAEA was there between 1994 and 2002 North Korea did not extract plutonium. It was after 2002, when the inspectors were gone that North Korea removed plutonium.
With the Bushehr reactor under safeguards, the IAEA can monitor the amount of fuel that goes in and comes out. Using equipment that measures the radiation level of the reactor pool and measuring the amount of LEU pellets that go into the reactor, the IAEA can ensure that Iran does not divert any fuel for weapons. Also, as mentioned, the Russians are taking back all the spent fuel, meaning the Iranians will not be able to extract any plutonium. The fuel in the reactor is low enriched uranium, 3.5%, which Iran is already using in their centrifuges. The fuel cannot be diverted to the centrifuges, as that makes no technological sense.
Also, India and Pakistan never fooled the IAEA as there were never safeguards agreements in place in the first place.(India just signed a limited safeguards agreement in 2008) Plus, those states are not party to the NPT, Iran is. But, no mention Israel either, which is odd.
The 2007 NIE has been beat to death, but essentially what we said was Iran since 2003 has not had an active weaponization program-meaning working on high explosives that can compress HEU and form a nuclear explosion. But, the IC has stated many times that Iran could change its mind, and that Iran continues to enrich uranium.
Finally, again, John Bolton has no idea what the hell he is talking about. He has no credibility in my mind. It is amazing how he just ignores the facts.
Edit: I'm not the only one who thinks Bolton is a complete and total idiot:
http://www.foreignpolicy.com/articles/2010/08/18/reactor_reaction?page=full