Needless to say, any church, however "traditional" its theology, that gives aid and comfort to the bullying of gay students (or adults) is sinning gravely. I am not, however, persuaded that there are enough such churches to account for the prevalence of bullying. Unlike Dan Savage, I know some conservative Christians socially, and I can no more imagine them taunting a gay kid than pooping on the courthouse lawn.
Mainstream Christian teenagers (including white evangelicals of only ordinary kookiness), in my limited experience, are indoctrinated as fiercely into niceness as into any ideas about dancing and erections. Savage's calumny is something I could only have learned from the papers and the Armani-clad charlatans who populate them, not from my actual experience with American Christians.
Now that's not to say that there aren't plenty of exceptions. Maybe I'm even wrong, and the people I know are the exceptions and the Joel's Army black-belt level haters are ruling the hallways of America's secondary education institutions. In any event, notice how the whole point of Savage's polemic is to lump a respectful, if wayward correspondent together with the most vitriolic people who share his religious identity and, as if that weren't bad enough, pour all the blame for gay teen suicides on this person's head.