In this case, as in most SCOTUS cases (Bush v Gore excepted), the effect of the ruling is precedent. The issue is now, at what point is AL bound to follow Obergefell?
"Holding: The Fourteenth Amendment requires a state to license a marriage between two people of the same sex and to recognize a marriage between two people of the same sex when their marriage was lawfully licensed and performed out-of-state."
The argument is that this doesn't apply to them because they were not a party to the litigation? Even if this is correct (dubiously and also in the narrowest sense) what is the effect of Obergefell on Moore's administrative order to quit issuing SSM licenses? He seems to be running strait at a brick wall created by the Obergefell decision, because the US SCOTUS opinion will be follow by all 50 states. Judicial effiency requries that all under the jurisdiction of the opinion are bound by the opinion, otherwise there will be anarchy while the decision is broadly applied, and a colossal waste of judicial time in hearing the same legal priniciple for all jurisdictions.
Using Moore's logic, states can issue administrative orders that are contrary to the McDonald v Chicago holding, a 2nd amendment case made applicable to the states by the 14th amendment.