Last week, a court ordered a Russell County High School student who had been designated to pray at graduation not to do so. Students rose on their own and recited the Lord's Prayer during the principal's remarks. The student who had been designated to lead the prayer included religious messages in her remarks to graduates. That option is absolutely protected under the Free Exercise Clause of the First Amendment and there is nothing the Judge can do about it.
The Muslim student can say her own prayer but neither she nor the ACLU nor the Judge can stop student initiated prayer that is not part of the official program.