Functional atheism is no 'neutral' stance on this. What is being taught is that only atheism is intellectually credible, and this is not by accident, this is deliberate.
It also is not evenly enforced. Going back at least to the 90's, special provisions have been made for Muslims to pray in schools, while Christians have been cracked down on, sometimes even just for having a Bible with them.
This is not a matter of neutrality, this is a matter of no longer banning everything except religion acceptable to leftists, IE atheism, agnosticism, and Islam.
Show me public schools which allowed Muslim teahcers to pray in front of their classes, because I have not seen anything like your claim about Muslims.
And the Establishment Clause has been in the US Constitution from the beginning, because the Founders didn't want Protestants, Catholics, Muslims, or any other religion to be seen as favored by the US government, to keep religious strife and political issues stemming from religion from tainting the US gov.
You can call that 'state atheism' if you wish, but the fact is the Founders of the US wanted a secular nation and a secular gov for good reason.
ignoring religion and questions about it is the best way foster strife between religions. Children need to be taught to be fearless in asking questions. They also need to understand that some questions are not easily answered and many religious ones are.
Preventing a person from prayer is wrong.
A person praying is NOT pushing said religion on another no matter where it takes place.
If an instructor is interrupting class to "grand stand" their prayer...that's wrong. I'll be with you in opposing that, unless it's a religious school of course.
Learning about religion is what church is for, and something the parents should cover at home; it is not the wheelhouse of public schools or their employees.
If a public school employee wants to pray alone on their lunch break, away from students, that is fine and protected. What is not protected is doing so in front of a class of students, who the teacher has sway over.
Parent's can send kids to religious schools if they want a religious based education with prayer in the classrooms; that is not what public schools are for or about.