The law does not trump the constitution. It's the other way around. Congress has no right to pass law that requires you to adopt a specific religion. Separation of church and state is nowhere in the constitution, the Bill of rights or the declaration of independance. Nowhere. And regardless of what has been imposed upon this judge and the state of Alabama, if it is unconstitutional, I say as our forefathers said. 'The court has ruled, now let the court enforce it's judgement.'
If you don't have separation of church and state (a phrase that I believe was first attributed to Thomas Jefferson, who wrote the Declaration of Independence and was heavily involved in the drafting of the Bill of Rights), then the establishment clause will become meaningless and unenforceable. As for your last sentence, it would be a complete, unmitigated disaster for the rule of law -- and a violation of his oath to uphold the federal and Alabama constitutions -- for the Chief Justice of the Alabama Supreme Court to take that position.