The reply of the Synthese editors-in-chief to the petition is now available here. (UPDATE: That site is now down--there is a copy here.) It is, I am happy to say, more substantive than their earlier response to the Guest Editors, and provides some additional information. It does not, however, appear to indicate that either an apology or retraction of the disclaimer is forthcoming.
In addition, The New York Times has a short piece on the affair, which also provides some additional details.
It does seem clear from these materials that there were only two "offending" articles in the issue, the sweeping character of the disclaimer notwithstanding.
I am travelling at the moment, but I did want to get this information into circulation. I will open a thread for discussion Sunday afternoon.
ONE MORE: Obviously, the author of the NY Times article was suckered by Beckwith's whitewash of his long involvement in the Intelligent Design movement. I'll have more to say about this later.