The phrase above simply states that religion is not going to be controlled or prohibited by the government in any way.
The act which inserted "under God" to the Pledge did exactly that. It made a law respecting the establishment of a relgion. If you're going to split hairs and say that the word God does not equate to religion, that's just silly. But the Pledge of Allegience is a nationally-mandated daily occurrence, and it made reference to religion. No amount of creative interpretation can change that fact.
The fact is that when it was inserted into the Pledge, it was done so by the Government in a carefully orchestrated attempt to stamp out atheistic communism. Think 1950's, think anti-communism... And read the words of Dwight Eisenhower when he signed it:
"From this day forward, the millions of our schoolchildren will daily proclaim in every city and town, every village and rural schoolhouse, the dedication of our nation and our people to the Almighty."
Go ahead and try to tell me that's not "making a law respecting the establishment of religion."
Look, I think the dude who took this to court is an idiot, and the words "under God" don't offend me, as I do believe in a higher power. The verdict WILL be overturned, though by the letter of the law, the Pledge is, in fact, unconstitutional. If someone challenged it high enough, and the judicial system worked as it should, either the Pledge or that phrase in the constitution would have to be ammended. They are in direct contrast, and no reasonable interpretation can say otherwise.