If i may extract quote from the message you replied to: As you know, I have refused to send McIntyre the "derived" model data he requests, since all of the primary model data necessary to replicate our results are freely available to him. I will continue to refuse such data requests in the future. Nor will I provide McIntyre with computer programs, email correspondence, etc. I feel very strongly about these issues. We should not be coerced by the scientific equivalent of a playground bully. I will be consulting LLNL's Legal Affairs Office in order to determine how the DOE and LLNL should respond to any FOI requests that we receive from McIntyre." (emphasis added by me)
I do agree with you that transparency is the litmus test of good science. At the same time, catering to that can lay you open to abuses from, well, trolls.
As an analogy, suppose I had a bee in my bonnet about Linux security and I kept demanding that Linus send me copies of his binaries every time he did a new commit. He would rightly tell me to get the sources and build it myself and leave him alone. and in turn I could post lonely rants along the lines of 'why won't Linus Torvalds come clean about Linux security'. It would be quite meaningless, but it would sucker in some people. If I was sufficiently clever I could probably get quoted by someone at Microsoft or in the BSD camp.
The parallel I am drawing here is to the public datasets and methods laid out in published, peer-reviewed papers. If McIntyre is so sure that either the methods or the datasets are flawed, why not follow the established practice of writing to the journal and challenging the paper, or even submitting his own analysis of the public data and explaining how it improves on existing analyses? Instead he posts in some minor journal which is not part of the scientific corpus, not a hard science journal, and has been widely accused of lax publication criteria.
One of the things that really bothers me about the skeptical crowd (as opposed to individual skeptics) is that they employ a lot of same kind of arguments as the proponents of 'intelligent design' do, claiming there's an ivory-tower conspiracy that silences all dissenting views and shuts them out of publication. Any time you have a bunch of people going 'OMG teh conspiracy', it's time to whip out the old bullshit detector...and all too often, comparing their claims with the published literature sends the BS detector way into the red.