I'll note that Wikileaks is wrong to assert that the Foundation removed the stories. (And Slashdot is wrong to repeat this assertion.) If that had been our method of operation, I could have removed the stories myself. Instead, we went to great lengths to explain what our legal concerns were, privately, to representatives of the community.
The WMF expressing legal concerns about the stories is effectively identical to the WMF removing the stories. The WMF wants the stories gone, the stories go - that's the short of it. If the general counsel of the WMF tells you there are legal concerns regarding one of your articles, you delete the article, you don't have any say in the matter, regardless of whether or not the WMF actually demands deletion.
That said, the WMF removing stories because of legal concerns has always been accepted (albeit reluctantly) by the community as something the WMF has to do. The WMF has a responsibility to obey the law, whether we like it or not. There is a big difference between removing the articles due to legal concerns and, as Wikileaks seems to claim, censoring articles critical of Wikipedia. As long as it was just the former (and I have no evidence to suggest otherwise), I have no problem with it.
I think the claims about losing CDA protection stem from a simple misunderstanding of terminology. When the CDA talks about publishing something, that refers to the bit where someone presses the "submit" button. When Wikinews talks about publishing something, the refer to the bit where it's decided that an article is ready to be removed from the "in development" section. The articles were, as I understand it, removed inbetween those two stages. As far as the CDA is concerned, the WMF stepped in post-publication to remove content they saw a problem with, which they are certainly allowed to do.