I agree the law should be changed, but that property is not "public" property, it's private property owned by the ministry and rented out for certain occassions, but it is still part of a church. They have their Christian standards, and that includes not doing business in a way that contradicts their Christian knowledge. This is a trampling of the members of the ministry's First Amendment rights, period. No state law can take away your constitutional rights--well, that used to be the case, anyway.
As to free exercise, the LAD is a neutral law of general application designed to uncover and eradicate discrimination; it is not focused on or hostile to religion. To the contrary, it carves away exceptions on behalf of religious organizations Respondent can rearrange Pavilion operations, as it has done, to avoid this clash with the LAD. It was not, however, free to promise equal access, to rent wedding space to heterosexual couples irrespective of their tradition, and then except these petitioners.
IOW - the church agreed to the conditions in order to obtain a tax exemption, then violated that agreement.
After the incident, they restructed and, as the judge conceeds, they CAN now prohibit such ceremonies on thier property.