Not at all. The photographer can still choose not to enter into a same sex relationship or marry someone of the same sex. Photographing a same sex couples does not infringe upon where they may worship, or what religious moral views they may hold. Conversely, denying the same sex couple service amounts to projecting one's religious moral views onto the couple, which does deprive them of free exercise.Your thinking is backward yes?
In states with anti-discrimination laws that include sexual orientation, these suits will continue to arise. The rhetoric on the part of those claiming infringement of their free exercise of religion are lacking in rational foundation. Providing a service to someone who holds alternate views on religion or morality does not violate the proprietor's free exercise. Such an argument is laughable.