The school’s policies lost it a tuition, and the author’s tuition went elsewhere
I have no idea how things worked at the particular school described by the author, but one possible solution would’ve been to let the student (with parental agreement) opt out of the daily Bible Studies / Doctrines Of Faith class, while still taking all the mandatory courses in English, history, civics, and STEM-stuff.
Over the years I’ve met numerous Protestants (mostly African-American) and even one Jew who attended Roman Catholic parochial schools under exactly these conditions. The local public schools sucked, and the Catholic schools had a certain number of openings for non-Catholic students, who were exempted from the “papist indoctrination” class unless their non-Catholic parents specifically wanted to opt them in. (At a Catholic school, the Religion classes will in some grades be focused on doctrines generally accepted by all Christians, and in other grades focused on things highly specific to Catholicism — like learning about transubstantiation when preparing for First Communion, for instance.)