If you mean, where should he go to during the religious assemblies, the answer would presumably be - the same place his sister goes to.
I assume that throughout their school life OP will be happy to collect her children during all lessons regarding all aspects of religion and various religious festivals. Or does she expect school to lay on extra staff a few times a week for her children?
There are many (probably the majority) of families who have no interest in religion. Most parents are happy for their children to learn about life that doesn't necessarily involve them.
What if her children would like an element of religion in their lives? OP is preventing them from making an informed decision, because of her own views.
There are children from many differing religions, and none, who attend religion based schools. My DD attended Catholic school. We are athiest. Her best friend through school was a child of Muslim faith. Religion aspects in school have made no difference at all to their religious beliefs. And they certainly haven't been harmed by learning about the lives of Catholics, Christians, Muslims, Jews, Sikhs, Hindus, Jehovahs Witnesses.....
Should a child who has no interest in science or PE be removed from those lessons? Or should they be involved in subects they have no interest in because these subjects are on the curriculum - the same as RE.