Look at the link below. It clearly lays out the fact that the Boy Scout's first amendment right to freedom of association trumped the State's decision to force them to accept an openly homosexual troop leader.

Brown v. BoE limited the discrimination public entities could engage in and did away with the doctrine of separate but equal. It did not have an effect on private entities. Public schools were desegregated. Public pools were desegregated. Public busses and trains had their seats integrated.

Private companies, truly private companies that did not accept any public money, could continue to do as they pleased. And they did.

Whatever your beliefs on the essence of christianity, they don't matter. Each church is a private organization that is free to define themselves. If they accept public money for something, to provide a service, then they must follow public policies in doing so, but as for their membership and the rights and rituals they perform within themselves, the government has no business telling them what to do.

Let's take another example. It is known that smoking cigarettes leads to lung, and other cancers. Many state and local governments have therefore banned smoking tobacco products in public areas for the public's safety. They have not banned smoking in private clubs, where members know that smoking is allowed. They have not banned smoking in private homes, where the owner/renter/individual makes the choice.

Do you see the parallel?