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There’s something off-key about that for the Skarins, who are atheists in a predominantly Christian town...sounds as though they want a law to prevent the rest of the town from the free exercise of their religious beliefs - the First Amendment specifically forbids such laws....

I imagine the Skarins would be offended by this Revolutionary War Battle Flag too:

Gostelowe Standard No. 10, c. 1776
Many battle flags of the American Revolution carried religious inscriptions. More examples at the Library of Congress

If the girls are in choir they can just not participate in the "offensive" song. We have Jehovah Witness children in school everyday who don't participate in the flag salute or the school Christmas pageant, etc.
These girls have a right to believe as they like, however no one is forcing them to participate. I think if this is a tradition in this school, they knew well in advance that they would be singing the Lord's Prayer during graduation excerises. Our government is based on Christian principles, it says right there on our money "In God we Trust", its no secret to anyone living here. You can believe what you like, but America is a Christian nation. If you don't want to participate, don't, but don't expect the rest of us to cater to your "needs".