First, businesses aren’t allowed to refuse services to people based on sexuality. Religious groups aren’t allowed an exemption to that rule and in the UK the Catholic church decided to close down its adoption services because they weren’t allowed to discriminate in terms of placing children with same sex couples.
But actual places of worship are a tolerable exemption. They are places where people express their beliefs and even if those beliefs are at best out dated and somewhat distasteful to mainstream society it’s reasonable to permit people too use their own spaces to express their beliefs. Personally I don’t believe religion is any excuse for exemption to the law but I think this point is a reasonable political settlement. People who go to church do so believing they’re engaged in some spiritual significant practices and forces people’s hand in what is or isn’t legitimate in their religion is perhaps a step too far.