Schools should be free of religious instruction; that doesn't mean intolerance. Teaching of religion as history/cultural studies yes - assemblies with prayers, state funded 'faith-based education', no. If Muslim, Sikh, Hindu, and Christian families want to educate their children about their religion outside of school, fine, no-one's stopping them. Most if not all of the Muslim, Sikh, Hindu children in my class go to places of worship/religious schools in the evenings/weekends.
Wrt to sex, it's not about the parents, it's about the children. They have a right to be educated about their sex, sexuality, their bodies and their emotions. To deny them that due to their parents' religious belief is harmful.