The most important thing is that the health of our intellectual environment is damaged when we start throwing around terms like "bigotry" when we don't have a proof that the view is wrong that is so strong that no one who takes the opposing view can be anything but bigoted. The charge of bigotry is an irrationality charge and, as such, requires a very high standard of proof.
What would be required would be evidence not only that there is nothing wrong with homosexual activity, but evidence that anyone, either on theological grounds or any other grounds, who thinks homosexual acts are wrong or sinful is in the grip of bigotry. Unless you want to go the "God Delusion" route (which would require a whole different set of APA policies) you are going to have to think inside the theological box and show that no reasonable person operating within a Christian framework can conclude that homosexual activity is sinful. The insitutions that are being targeted in the petition are colleges like Wheaton and Calvin. Their contributions to the philosophical community are enormous, as, I think, most people realize. That alone is good reason to think, once, twice, three times, and four times before tagging them with bigotry.
And even where there is bigotry, dialogue, not official censure, is the best remedy.