Of the four churches I have been to Central Texas, three of them were pro-LGBT and had members involved in campaigning (all Lutheran churches btw, who made up probably the largest group in this region followed by the Catholic church). This was also 10-26 years ago. All of the churches donated to charity, ran food banks & soup kitchens, provided disaster relief after flooding, fires and tornadoes we get here, and only one of them was anti-Obama... and that church fell apart. The other three were all very progressive ideologically and still are, with the last one I was a part of hiring a lesbian pastor last year. The church I was in in New Mexico was much the same, and had a gay pastor when my family was going there. Likewise the different Sunday school groups often discussed topics ranging from theology to social issues and politics, and there was debate... it wasn't everyone just agreeing that "God... obama sux...dem geys faggots... etc. etc.". On Texas State, the campus Lutheran and Roman Catholic organizations are heavily involved with the LGBT movement. I would argue the majority of my progressive ethics are a result of my church upbringing, which clashed with the ultra conservative culture I grew up in.
And yet again, I will have to say that is all irrelevant because both what you said and what I said prove my point; churches are social institutions that enable the easier facilitation of spreading social institutions and community involvement, either positive or negative. When I went through Conformation, the ideology taught by the different teachers varied; there was one who openly promoted safe sexual behaviour and one who was a white woman who married an African man, and others who taught more "normal" church values but still generally progressive, including to not judge people for their race, culture, sexuality, social standing or whatever... things that would not have been taught to me in other social institutions (school & school related groups).
Just because we are atheists doesn't mean we have to plug our ears and scream that nothing good could ever come out of religion despite all evidence to the contrary and at risk of contradicting ourselves when we say the church holds any sort of social power.