Legal Question in Employment Law in California

Legal? Of course.

Churches and their related organizations are specifically exempt from the discrimination laws. For patently obvious reasons, they can exclude non believers. They can make active membership in their faith and church a requirement. They can impose and enforce morals rules, dress and behavior codes, etc. It's called 'freedom of association', and 'freedom of religion' as protected in the First Amendment to the Constitution. Government has NO authority or right to interfere with religious decisions like that, including making any rules or laws about 'discrimination' apply.