Their story hits very close to home with me, as I went through a very,very similar process with respect to a comment (PDF) and reply (PDF) on the "shameful article" on hurricanes and global warming that I co-authored in 2005 (PDF). (If my emails ever get hacked you'll see that ugly episode from the inside.;-) That situation had a positive outcome only because at the time I protested efforts to deny us a right to respond in accordance with journal policies and threatened to go public with the improper efforts at stage-management. I am sure that these sort of shenanigans go on in academia more than we'd like to admit, however that does not justify them.
What these episodes reveal is an effort by activist climate scientists to stage-manage the peer review process much like how one might manage a partisan blog for public consumption. The blog management philosophy of Real Climate was described as follows in the CRU emails:
I wanted you guys to know that you're free to use [the RealClimate blog] in any way you think would be helpful. Gavin and I are going to be careful about what comments we screen through, and we'll be very careful to answer any questions that come up to any extent we can. On the other hand, you might want to visit the thread and post replies yourself. We can hold comments up in the queue and contact you about whether or not you think they should be screened through or not, and if so, any comments you'd like us to include.While bloggers are of course free to operate their turf as they see fit, whatever one's views of climate science, climate policy or the Douglass et al. paper, we should all be able to agree that efforts to stage manage the peer review process are not good for science, however they might be justified.
You're also welcome to do a followup guest post, etc. think of RC as a resource that is at your disposal to combat any disinformation put forward by the McIntyres of the world. Just let us know. We'll use our best discretion to make sure the skeptics dont'get to use the RC comments as a megaphone...