I'm absolutely with the school on this. What I would describe as "indoctrination" would be parents who implant the idea in young people's minds that gay people are outside of normal society and their relationships are, at best, abnormal and inferior and, at worst, an abomination. Homosexuality is no longer illegal but discrimination based on a person's sexuality is, so, apart from the fact that it's wrong to ignore discriminatory behaviour, it's important that children should consider not only the ethical but also the legal perspective.
I believe that there should be acceptance of dress codes and religious beliefs in public life. However, I also think that when religious beliefs and cultural norms impinge on the lives of other minorities and lead to intolerant attitudes and behaviour directed at them, that needs to be addressed.
I would just mention, though, that I'm fairly sure some parents in other schools have objected to their children having sex education lessons dealing with subjects such as homosexuality, contraception, etc., so this attitude is not exclusively a Muslim one.