There may be statutory law or state constitutional law that requires the school to exempt students whose own exercise of religion is burdened, and the potential for burden is a good reason for not structuring an assignment like this. In any case, the school might want to avoid assignments like this because it's not how the people in the community want their children to be taught. And in the end, the school acceded to parental pressure.
The linked article (in the NYT) says the Augusta County School District said it received phone calls and email that were "voluminous," "profane" and "“hateful." There was "no specific threat of harm to students, schools and school offices," but the cancellation was done — as the Times put it — "out of an abundance of caution."
Despite the outcry, the district said it would continue to educate students about the world’s religious diversity as required by state education guidelines but that “a different, nonreligious sample of Arabic calligraphy will be used in the future. As we have emphasized, no lesson was designed to promote a religious viewpoint or change any student’s religious belief,” it said.They should have figured that out in advance, and it's distressing to see those who objected portrayed as hateful and potentially violent when they are attempting to protect their own religion. What if Muslims in the community objected to a lesson about Christianity that demanded that students read the Nicene Creed out loud? Would the New York Times portray the Muslims as potentially violent? I don't think it would. In fact, I think the NYT would portray the reading aloud of the Nicene Creed — "I believe in one God, the Father Almighty... And in one Lord Jesus Christ, the only-begotten Son of God" — as a violation of the Establishment Clause.
The NYT quotes one of the parents as understanding the assignment to be an instruction "to denounce our Lord by copying this creed of Islam," which is "an abomination" to her family's faith and that the school had simply "cloaked in the form of multiculturalism." And therein lies the problem. How do you know what the school is really doing? And quite aside from what the school meant to do, there's the question of how it is perceived, which is an important part of Establishment Clause analysis.