I was going to write a post on the subject of the APA petition, but Andrew beat me to it. That said, I notice that on the Leiter thread, people in support of the petition are quite certain of the rectitude of their views, whereas people urging caution, or rejection, of the petition, use much more cautious/defensive language. Moreover, almost all of the people who support the petition use their real names, whereas many of the people opposed to it, or who urge caution regarding it, write in anonymously.
Assuming I'm right about this, I wonder what it amounts to? I think this:
Many, if not all, traditionally Christian (and, I imagine, Jewish and Muslim) philosophers are afraid of posting their thoughts on this matter. First, they are afraid of being personally attacked. "Fear of personal attacks" should be construed broadly: it doesn't refer just to being scared of what your colleagues will say or think of you; it refers also to fear of the emotions that will arise within you upon being personally attacked. That is, you may be afraid that you will write something in emotion-induced haste.
Second, I bet a lot of traditional Christians are in fact unsure what is wrong with same-sex relations. They accept that people should not have sex with members of the same sex, and/or that people should not marry people of the same sex; but they don't really accept or understand any of the rationales offered for why. Or perhaps even stronger, they side with a lot of the philosophers posting in Leiter's thread, and their beliefs on this score are an abiding source of tension for them.
Third, assuming that philosophers in support of the petition will in fact personally attack someone who publicly defends the propriety of the APA's position, is this behavior warranted? Many philosophers, including Christian philosophers of all stripes, seem to think that there are cases where personal attacks are appropriate. I can't remember where she said this, but I recall G. E. M. Anscombe writing that there are some positions so corrupt that they shouldn't be met with arguments but rather with disgust, condemnation, or something of that sort. I'm actually inclined to disagree with Anscombe on this score. I think that such condemnation is rarely productive in philosophical debate, and I think there are indeed good arguments that can be offered in favor of lots of positions that most people hold unreflectively (e.g., a lot of people look at necrophilia with disgust, and think that no one should engage in it. But why? I bet a lot of people won't be able to offer very good answers to this, other than just to say that it's disgusting. But a clever philosopher could quickly, I think, move most people to aporia over this). In other words, I think a lot of the philosophers posting in Leiter's thread are not behaving as they should. But I might be rash in saying this--after all, how would I feel if people were defending philosophy departments that, say, required their theistic students to sign statements giving up their theism under threat of expulsion? I should think I'd be very dispirited if even a few philosophers supported such a notion, and I would quite possibly describe them as bigoted. Of course, under such circumstances I don't think it would be appropriate to use such language, even though I think it would be factually correct.
EDIT: I should add, in elaborating my third point, that I thought it inappropriate to make personal attacks on people at least when you are trying to convince them of the wrongness of their position. Thus, calling discriminating Christian universities bigoted in the comments section of The Leiter Reports is not itself inappropriate, and, to the extent that the language is factually correct, fine, perhaps even to be encouraged. Now that I think about things a little more, though, whether it's appropriate to call a person bigoted depends not only on whether he actually is bigoted, but also on whether such remarks are liable to convince him. There could definitely be some people who, when described as bigoted by people of good will, will rethink their positions. In such cases, then, calling a spade a spade is fine, perhaps even recommendable.
Nonetheless, though, I think there's a kind of civility that it's important to maintain in such arguments, at least when you're writing to someone. You don't want someone to accept your position out of fear, and you don't want them to reject your position out of defensiveness. Instead, you should want, if you're a philosopher, your interlocutors to focus on the reasons you offer for your position rather than on the consequences that their beliefs and conduct will have on your assessments of them.