I never suggested standing by silently; by all means, make it crystal clear that you disagree. But no matter how passionately you feel, when you stoop to ridicule or baiting, you undermine your position by sounding rabid rather than reasonable. If the Christians are saying "Even though we disagree, we'll still accept you", while the Atheists just hurl insults at the Christians, who comes out looking better? It's simply more effective to maintain a civil tone, lest your noise overwhelm your signal.

Also, consider this: When a person is caught in a conflict between their sexual orientation and their religious views, it might, in fact, be quite comforting to know that their religion and their religious community are not going to ostracize them for it. They may still want to remain a part of that faith, or at the least, have ties to it that they do not wish to sever.