Depends on the church in question. I know gay people who are accepted by their congregation, and churches that don't have issues with gay people at all. The biggest LGBT youth group in my city is organized by and hosted in a Christian church.
The institution of traditional religion played a social role in Western societies that has not been adequately patched over by anything else yet. Even as a non-religious person, I do take seriously the hypothesis that the decline in regular church attendance accounts for some of the social isolation crisis. (That is of course, hardly the whole picture. A similar argument can be made about union meetings or youth clubs, both of which have also declined significantly in regular attendance over the last half century.)
