Yes, the Supreme Court made a ruling citing separation of church and state which is not found anywhere in the constitution.
The Supreme Court also once ruled that a man could own another man as legal property. That is also not in the constitution. Was that the correct ruling or were they wrong?
The constitution simply says that Congress will not endorse nor prohibit religious expression. It doesn't say that people cannot voluntarily pray in public buildings. At one time, the U.S. Capitol was also used as a church building, hosting church services weekly. Just because the Supreme Court says separation of church and state is constitutional doesn't mean it is.
The school received a letter threatening a lawsuit. They do not have the money to fight it, so they had to stop even though they did nothing wrong or illegal.
I don't believe in forcing religious beliefs on to others against their will. However, I believe very strongly in free expression and the tolerance of others' right to express themselves. If one is intolerant of another person praying, then it's not the fault of the one saying the prayer.
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NB,
The schools (multiple) clearly were breaking the law. I guess you failed to see the video link I provided with the school principal saying that they knew what they were doing was illegal. You keep repeating yourself about the legality of mass school prayers but have yet to cite any case law to support your claim, so I will.
The Supreme Court has so far made EIGHT separate rulings from 1952 to 2004 affirming that school-sponsored prayers (a religious activity) in public schools is a violation of the Establishment Clause and constitutionally impermissible. In fact, it gets worse for theocrats every time they choose to fight against what is now 60 years of Supreme Court precedents on school prayer, that basically says that religion can only have a sharply limited role in our public schools.
Look up: Santa Fe Independent School Dist. v. Doe, 2000
(in a 6-3 decision) The Court held that the policy allowing the student-led prayer at the football games was unconstitutional. The majority opinion held that the pre-game prayers delivered "on school property, at school-sponsored events, over the school's public address system, by a speaker representing the student body, under the supervision of school faculty, and pursuant to a school policy that explicitly and implicitly encourages public prayer" are not private, but public speech. "Regardless of the listener's support for, or objection to, the message, an objective Santa Fe High School student will unquestionably perceive the inevitable pregame prayer as stamped with her school's seal of approval." - Justice Stevens (a Christian, nominated by Gerald Ford)
Look up: Lee v. Weisman, 1992
"As we have observed before, there are heightened concerns with protecting freedom of conscience from subtle coercive pressure in the elementary and secondary public schools. Our decisions in [Engel] and [Abington] recognize, among other things, that prayer exercises in public schools carry a particular risk of indirect coercion. The concern may not be limited to the context of schools, but it is most pronounced there. What to most believers may seem nothing more than a reasonable request that the nonbeliever respect their religious practices, in a school context may appear to the nonbeliever or dissenter to be an attempt to employ the machinery of the State to enforce a religious orthodoxy." - Justice Kennedy (a Christian, nominated by Ronald Reagan) writing for the majority
Regardless of your opinions and interpretations on these matters NB, what the schools were/are doing is against US law. Period. I ask you again to please prove otherwise, with something more than your opinions or beliefs.