Those who run school music programs should consider the consequences of their choices of music on the system as a whole, and be careful to select music that is not designed to indoctrinate children into Christianity or any other particular religion. Historically, it has been abuses of the system that result in regulations and lawsuits. Nobody expects to convert a non-Christian child to Christianity by having them sing these songs. But they are a part of American and even world culture, and as such it is justifiable to include them in a program of music education. As should good music from all cultures and religions.
Great music belongs to humanity as a whole.
It transcends sectarian divisions and draws us together in appreciation and awe for something far greater than any individual composer's ability or beliefs. To deny our children the opportunity to perform, and thus experience this music as they can do in no other way, is to deny them their heritage.