Here's the key: what if the Judge was faced with interpreting a law that was "legal" but not in accordance with his religious beliefs? Would it be okay to overturn it because God told him to? The Judge cannot use his office as a pedestal from which to trumpet his beliefs (you'll notice the other 8 Justices did not agree with him). The statue wears the imprimatur of the state's highest jurist - it's hard to say therefore that the state is not endorsing a certain belief. Interestingly, witnesses are told to put their hands on "The Bible" when they swear in to testify - but, you're allowed to "solemnly swear OR affirm" thereby giving the atheists an out. I've always thought that Bibles should be taken out of courtrooms - but then again, I have alterior motives.
To answer a question, the 14th Amendment passes the 1st Amendment's contents onto the states, so it's not just a federal issue. Also, and although it's a good point, the fact is that all judiciaries are "established" by the Legislature. Federally, we call them "Article III" judges because, uh, that's where they come from in the Constitution. With the states, it's typically the same. Also, the Alabama District Court had a nice little ditty on this:
"The Chief Justice placed the monument in the Judicial Building Rotunda under his authority as administrative head of Alabama's judicial system. Ala. Const. amend. 328, § 6.10 (administration); Ala. Code § 41-10-275 [*1315] (1975) (leases). His placement of the monument, therefore, has the force of law. The Chief Justice is the only person with the authority to place the monument or remove it, authority given to him by the laws of Alabama. To say that his actions in placing the monument in the Alabama Judicial Building does not constitute a "law" obfuscates the truth of the situation: the monument was placed in the Judicial Building by a state official, acting in his official state capacity, under powers granted to him by state law."