You pose a difficult situation. The First Amendment prevents any law against both the establishing of, or the free practice of religion. This has served well to keep religious wars out of America. Religion is guilty of preaching hateful things, and blessed by preaching loving things, it is not one thing, but many. A belief, and willingness to think it, is the basis of a freedom of conscience.
Considering the history of religion throughout the past two or more millennia, it is perhaps best to give it a pass, on some things, but not approval. From freedom of conscience, comes all new thoughts, which sooner or later must be expressed, hence freedom of speech. Speech must be given to others, those that agree will gather together, hence freedom of assembly. If they feel abused, as LGBTers have, they have the freedom to petition their government for their grievances. One thing grows from the other. All guaranteed by the First Amendment.
Religion, for all of its myriad qualities, has been a fountain of ideas, both for and against, allowing some to believe, and letting them do so, is just another form of live and let live. So long as it keeps the peace, time will end old ideas, prejudices, and misunderstandings, but it is ever a work in progress to make a more perfect (fill in the blank).