Those are the military making accommodation rules versus a municipal employee doing their job guided by religion. There are often very different takes on Constitional rights while in the military and what is done within the organization. Like it or not, SCOTUS ruled on it. If they determined there is a constitutional right to marry, it is not up to a clerk employed by the government to dole out rights based on their religious convictions. Period.
Again, if the Feds want to shove some rights that are counter to a majority of human culture since the dawn of civilization down the throats of states (almost all of which have had their citizens vote against it), then that is a two way street, and I want my CHL and all its rights extended to wherever I am in the US. This will include open carry after Jan. 1. If two dudes can be married and openly make out at the mall as a constitutional right in every state,mthe my ability to bear arms should also not be limited to the borders of Texas.
By the way.......I don't agree with how this decision was done. I think marriage should be defined by your Church, and contracts of union should be allowed in every state, with each state setting their own parameters for those unions as to how many people can enter into them (including age, and relationship).