Those parents should enroll their kid elsewhere or hire a private babysitter. After all the concessions the school would need to make to appease them it would more or less become a personalized curriculum for their kid. From a CBC article:

They also objected to celebrations of Easter and Valentine's Day, holidays they believe have become too tied up in materialism and consumerism.

So what, on Valentine's day when they're gonna have the teacher print out a picture of a house for their kid to color while the others color hearts?

And the parents themselves seem to be picking a fight and being assholes. From a CBC article on this:

For instance, when Mangel learned the school planned to include clay elf decorations in its December festivities, he wrote an email to the board objecting, and suggested some "atheist Christmas ornaments" that would better represent the views of his family.

That included one that simply says "Skeptic," and another that depicted the World Trade Center in New York with the caption "Atheists don't fly airplanes into buildings."