Nicely put. This is why I don't prefer an equal-protection argument in this case.
Wait a minute, are you telling me that if Moore had not put the Commandments up, and simply insisted upon leaving the rotunda area unadorned, and refused to allow citizens to put up displays of their own, he would be just as much in violation of the Constitution as he is now? That's how your post came across to me.
It's a discretionary act on his part. He's not required to decorate the rotunda at all, but once he does, it cannot be exclusive to his particular viewpoint in matters of religion. If he had chosen to decorate the rotunda in a secular manner, he could have done so in whatever manner he sees fit without ever implicating the establishment clause, which has been the source of his troubles from the beginning - nothing in the First Amendment prevents Judge Moore from using his office to stake out a position on secular issues, after all. Indeed, his job requires him to do exactly that. But once religion becomes the subject, the establishment clause comes into play, and Judge Moore has less of a free hand than he might otherwise wish for, by virtue of the fact that he's an agent of the state.