If there is no harm in exempting him from saying the pledge against his religious beliefs then the government cannot require him to do so. So, he has a good freedom of religion case against the school district.
Court cases have involved Amish refusing to send kids to school past 8th grade violating compulsory attendance laws, Amish paying into Social Security, A couple covering the "Live Free or Die" slogan on the NH license plate, students saying the pledge or standing during the pledge, etc. All these cases were won by the individual/group challenging the law.