Ingo Brigandt's comment here deserves its own post:

Here is another petition, organized by those who are considering a boycott (as far as I know the plan is first have the petition and to decide whether to proceed with a boycott depending on the response of the editors-in-chief): http://www.petitiononline.com/Synthese/petition.html

This petition is stronger than the two created by Eric, as it includes the call to retract the disclaimer. The latter is to my mind non-negotiable at least for the following reason. In his response to Barbara Forrest (published in Synthese, but after the special issue), Francis Beckwith uses the issuing and unusual nature of the disclaimer as a major argument against her paper.

Some creationists instrumentalizing the disclaimer in some venues is not surprising, but it is not just the case that the EiCs opened the door to this (as an unfortunate side-effect), but they obviously approved Beckwith's response after having scrutinized it, so that the EiCs approve of using the disclaimer as an argument (even in their own venue).

Combine this the EiCs stating in their response to the boycott plan that "several articles included in the special issue contained language that is unacceptable" (my emphasis), responding to the guest editors' account by making explicit that the problem was not only Forrest's article. So by now we have a clear license by the EiCs to use the disclaimer against any article in the special issue, which cannot stand.

A real danger with leaving the disclaimer as it is, or at least not mitigating Beckwith's use of it, is the extremely high probability that the next time Professor Forrest testifies to the LA state legislature (as she often does in these matters, and no doubt will soon in the debate on SB 70, which would repeal the stealth creationist Lousiana Science Education Act or LSEA), some ID partisan will claim she has been "refuted" in the pages of a prestigious philosophy journal and that therefore her testimony should be discounted if not ignored.

Philosophers and others outside Louisiana should never forget that this affair is far more than an intramural discussion of professional obligations, as seriously -- and rightly so -- as we take those concerns.

For there are real world effects at work here. Effects as real world as it gets: we're talking about a state law in which the work conditions of Louisiana public school teachers (who are our colleagues too, let us not forget), and the quality of the science education afforded Louisiana public school students, are at stake. Which makes it all the more admirable that in a climate of drastic budget cuts to higher education our colleague Barbara Forrest is willing to carry the fight against a Legislature and a Governor who have already passed and signed a stealth creationism bill.

UPDATE, M 25 April, 3:05 pm CDT: The eminent philosopher of biology Mohan Matthen has a powerful comment at Leiter Reports that should be read in its entirety. It begins:

I read the Forrest article in Synthese, and am having some difficulty figuring out why the EiCs consider it discourteous, impolite, or (most of all) unfair. The article is among other things an examination of the epistemology of ID theory, and in particular of whether inferences to intelligent design can be considered epistemologically on a par with scientific reasoning. It considers this question in the context of whether it is constitutional to permit the teaching of ID theory in public schools on the grounds that it is science, just as Darwinian evolution is.

In this context, Forrest provides a lengthy exposé of religious rhetoric by some of the proponents of ID theory, including some that predates their entry into the ID debate. This exposé is couched in emotionally charged language, to be sure, but only in response to what Forrest reasonably takes to be a public policy aim of the ID proponents and their own rhetoric....

The conclusion:

The Forrest paper is not an original work of philosophy, and is not intended to be. However, it is a powerful piece of contemporary historical research and is, moreover, quite astute in its exposure of philosophical fallacy. Even on a "pure philosophy" level, it is instructive to read of the perverted uses to which bad philosophical argument can be put. Moreover, its rhetorical temperature is perfectly appropriate in a work of this sort.