I know that people are concerned about this, but they're not taking into consideration the right that religious organizations have always had to "refuse service" (so to speak).
So, let's say that church requires for one or both persons in a couple to be a member of the church in order to marry. If they are approached by any couples who are not church members, they can legally refuse to marry those couples. (Also, churches aren't required to indiscriminately offer membership to anyone. They can set their own parameters for this). There are lots and lots of congregations that require membership for marriage. Many also require pre-marital classes before a marriage will be performed.
Additionally, there is usually little "commerce" involved in these circumstances. Most of the pastors I've known of do not charge for performing weddings for the members of their congregations. Sometimes couples will give a pastor an offering for this service, but the performance of weddings is seen as part of basic pastoral duties and is not charged.
Here's where there MAY be some confusion. There are Christian people who own wedding chapels. These are not CHURCHES, but places of business. These people make a living from officiating over wedding ceremonies. If a Christian pastor own a BUSINESS and refuses service based on anything that violates civil rights, this person and the business can be subject to a law suit based on these violations. So, if the owner of a wedding chapel refuses to marry a mixed-race couple, this owner could be sued. If there's a refusal to marry a handicapped couple...again, subject to the law. And, therefore, the same would apply to same-sex couples. But it's not because this person has a "church," it's because they own a business.
So, here's perhaps the need for concern: If there are pastors out there who have actual congregations but who perform weddings indiscriminately as a means of supplementing their incomes, they might need to either 1. stop doing that or 2. be prepared to marry same-sex couples.
Additionally, if churches don't have policies regarding membership or marriage within their churches, they might want to rethink that.