Richard G,
You are only paying attention to half of the "religion" portion of the first amendment. There are two clauses, the "establishment clause" and the "free excercise clause." It is the former, "Congress shall make no law respecting the establishment of a religion..." that is in play here. As has been pointed out, the Alabama Constitution contains similar language, but even if it didn't, this clause does apply to the State of Alabama through this section of the fourteenth amendment:
"No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States;"
There is a tension between the "free excercise" and "establishment" clauses, but it is fairly clear that a line has been crossed here. As pointed out earlier, Judge Moore can pray at home, he can pray at church, he can pray in the street (a "traditional public forum"), he can even pray at work, in chambers.
He can not, however, allow his official duties or the government facilities to be entangled with religion. The large granite monument of a specific set of religious rules in the entryway of a public building most certainly fits this description.
By the way, the Declaration of Independence is, in no way, shape or form the "foundation" of the Constitution. They are both important in a historical and political context, however, only the Constitution has legal effect, and the documents have little to do with each other.
Upchruch,
I doubt highly that this administration is going to "federalize" anything top enforce this particular federal order. It is also unlikely that Judge Moore will face jail time for civil contempt. The Federal Court order will likely be enforced by the leveling of fines against Judge Moore in his official capacity, which will be payable, I believe, by the State of Alabama.