I'm not interested in discussions on the pros and cons of vaccination. For what it's worth, I experience partial hearing loss as the result of a bad reaction to a vaccination when I was 16, but that hasn't made me "agin" immunisation.
What does concern me, however, is the issue raised in the original post - that state-funded schools are able to "opt out" of not just immunisation programmes, but also other programmes designed to benefit the health, safety and well-being of young people. If a school is completely privately funded, as much as I think they would be denying young people important information and access to services, they couldn't be compelled to do anything. However, if they are tax funded in any way, I believe they should not be allowed to opt out.
There are large high schools in areas near where my organisation works that refuse to engage with any sexual health services, that will not allow their students to be involved in teen pregnancy or teen parenting projects and have rejected offers from voluntary agencies to talk with their young people about issues including relationship abuse, sexual abuse, homophobia or sexual exploitation. All of these are massive issues for young people in these localities, but schools insist they "know best" how to deal with them, through moral and faith teaching alone.
One of my colleagues attended one of these schools and said she'd felt like a lamb to the slaughter when she went on to university because she had been so sheltered and was so ignorant of even basic information about sex, sexuality and risks.
I don't actually know if these two schools have opted out of the HPV vaccine or not, but I wouldn't be surprised, given their previous stance on any issues related to sex or sexuality.