The O'Neill revelations have put the Bush Administration in an offensive, rather than defensive posture. The Administration has rushed to conduct an investigation on the grounds that O'Neill's revelations may have been "sensitive" (note: that is NOt the same thing as "classified"). The Administration did not hesitate to grant such access to documents to Bob Woodward, of course, nor did they rush to conduct an investigation on the Valerie Plame affair (which did actual harm to our national security and is a truly criminal matter). Nick Confessore makes much the same point in TAPPED and frankly it's a devastatingly cogent argument.
To get a sense of the principled disagreement, I read Dan Darling's analyses of the issue, but I think he is making an error in equating the regular contingency plans drawn up by State and DoD with the specific policy objective of deposing Saddam as soon as the Bush team entered office. This is a significant distinction.
The relevant part of O'Neills expose are where he describes how he took his foreign policy and economic concerns to VP Cheney and was dismissed. O'Neill found that there was no policy debate as you wold normally expect. There was simply a-priori defined policy objectives, and the facts were chosen (cherry-picked) to justify that objective.
The bottom line is that ideology, not rational analysis of all available facts, is what drives the policy engine of the Bush Administration. And there is an ongoing culling of the ranks of anyone who does not step into line.