Which law made in pursuance of the Federal constitution permits two men or two women to execute a personal services contract under the sections of the Alabama (or any other state's) marriage code?
Even if Congress were to pass a law acknowledging the possibility that a same-sex relationship could be a marriage in DC and on Indian reservations and military bases, how does that law bind the states? It's certainly not a law "made in pursuance [of the Constitution] thereof".
The Civil Rights laws, although parts of them are of dubious constitutionality, were made to implement Amendments XIV and XV, and the power to legislate for this purpose was granted to Congress by the amendment process. That is most certainly not the case with Federal courts enjoining enforcement of state marriage laws, and even the Supreme Court has no proper basis to rule on these cases.
I'm not sure there is one. But if there were does a state have the Constitutional right to nullify that law by ignoring it. That is the question that was being debated.