My guess is that the two-word addition by Congress will be removed by the SC.
Legally, how could it not?
I'm not sure the Supreme Court will get a chance. The case is almost certain to be heard em banc by the entire 9th Circuit, and they might reverse the ruling. If they do, I doubt the SC would hear the plaintiff's appeal.
It would be an interesting case for the Supreme Court to hear. If they uphold yesterday's ruling, it would effectively ban the mention of God in anything relating to a government activity. That certainly would be consistent with the trend in decisions over the past few decades.
However, they could also take the opportunity to state that the Constitution doesn't require such an extreme prohibition, which would effectively reverse that trend. That would open up, once again, the controversies over Nativity scenes on government property, posting of the Ten Commandments, etc.
It would be an interesting case. If the Supreme Court upholds it, it's a slam dunk that IN GOD WE TRUST is unconstitutional as well. People can refuse today to recite the Pledge, but they can't refuse legal tender containing that phrase as satisfaction of debt. Similarly, the oath witnesses are required to take before testifying ("so help me God") would have to be immediately modified.
I am actually very happy that the court made this ruling yesterday because it forced the entire country to wrestle with these questions, and we need a final resolution as to whether the Government has to go to extreme lengths to avoid anything with even a vague religious connotation.