I don't think you're implying court decisions are right only if they agree with you, but your statement could be interpreted as such. There are those on the left who would present the same argument form the opposite perspective. Many feel SCOTUS placed George W. Bush into office against the will of the people. The point is, we are a nation of laws made by and enforced by imperfect and diverse people. Most of us have heard the old joke about opinions and lawyers. The Constitution (and John Marshall) has given the Supreme Court the final interpretation. If they say the sky is plaid, Congress can revisit the issue and clarify the language.
Getting back to the separation issue, the gist is government isn't to interfere with religion and religion isn't to dictate to government. Rather than allow a manger on the courthouse square, we have chosen to disallow all religious stuff. Saves making decisions when the neighborhood iman or rabbi asks to have a display.
The Doctrine of the Separation of Church and State is legalistic hairsplitting at its best/worst. It should be no surprise to anyone that lawyers "lawyer" and will twist (as is obvious) a plainly-written, historically-verified bit of prose to mean what they want it to mean. That doesn't mean it's justified or right. If that were the case, Dred Scott would have "settled" the slavery question, wouldn't it? The Supreme Court was wrong in its decision because it strained legal opinion to get to the conclusion it wanted, not because it properly interpreted the Constitution.
As to government having "chosen to disallow all religious stuff . . .(because) . . . saves making decision when the neighborhood iman(sic) or rabbi asks to have a display", it's not government's job to have ANY say in whether religious displays are placed in the public square or not. Traditionally, the menora has been displayed during Hannukah(sp?) right alongside the manger scene in public. Buddhas get displayed in Chinatowns. The muslims (and other religions) don't believe in having religious images; that's their faith and they're welcome to it. What no one has, is the right to be offended and go to court to force OTHER believers to take down their religious displays. That courts have chosen to rule against the First Amendment is more an indicator of political correctness and the encroachment of government on our civil liberties than an indication of the rightness of their judgment.
And, if Christians, in due course, become a minority religion in the United States and the muslims become the majority religion, Christians STILL will have the Constitutional right to worship freely, as the muslims have the Constitutional right to worship freely now.