I don't think the Boy Scouts issue had anything to do with the establishment clause. It was about equal access to facilities without discrimination on the basis of religion. The Boy Scouts argued during the homosexual case that they were a private group and therefore exempt from state anti-discrimination laws. Unfortunately, this argument bit them in the ass when they tried to defend their access to government bases where groups are not allowed to discriminate on the basis of religion. They're a private group, ergo no special rights to ignore federal law while taking federal benefits. (paraphrasing)
I do think that schools are allowed to have Christian and Bible clubs meet on campus. I know my high school had one in the 1990s.
I suspect there is a lot of misunderstanding and confusion surrounding the legal interaction between state and local government and state and local schools with religion. I also think people are jumping to assume the worst-case scenario when that is not always warranted. The situation is much better than many of us fear. In addition, I see no reason to make life harder for Muslim students to pray within the guidelines of their religion. I fail to see that as an anti-Christian gesture when every religion benefits from equal access!