The result of brown v board was that the American public school system was desegregated - black kids and white kids could go to school together. They were desegregated because it was found that the mandatory separation in place violated the 14th Amendment of the Constitution, and as a public institution, public schools must abide by the rules and guidelines set forth by our government. However, private school, even today, can set up parameters for their student-body. A private school can be all white, all black, male or female only, you name it, the school would not receive funding by the federal or state government. The same thing would apply to churches. There are no public churches, so any church can allow or deny any couple to get married. Today, a church can deny a inter-racial couple to get married, they can even deny a heterosexual couple marriage on any grounds that the church feels is valid. Churches can even hold, and have held, same-sex marriages.  Also, couple can get married through other institutions besides the church.     Allowing same-sex marriage would not infringe on the exercise clause of the First Amendment. What the debate is about is the United States government acknowledging same-sex marriages. It is not about integration into the church, it is about recognition by the government.