"Then he’ll be examined at GCSE in a topic he doesn’t believe to be true, which will set him up for failure (anyone commenting, please note that Catholic schools teach a VERY different curriculum to non faith schools)."
You do realise that being raised Catholic, in a Catholic Primary and then secondary I didn't have a choice where my devout religious parents sent me and although "Catholic" I had stopped believing in that religion by the time I was 12.
You just learn what to write that will get you marks, you don't have to personally believe anything, just write what the examiners want to hear. Same with class discussions, you don't tell everyone you don't believe.
We had a mini mass every week at the chapel on site, we had retired priests living on site, we had nuns and brothers in their brown Jesus sandals as teachers. If you ever said you were having doubts it just led to intervention by the retired priests coming to indoctrinate chat to you.
My children went to a CofE school and we just talked about all religions. You can do this at home, it is a conversation opener, what did you learn today at school? When they tell you about their RE lesson you can talk about it. Mine learned about other faiths, still atheist.
On homosexuality specifically, my sister was gay, went to the same school obviously. You just keep your mouth shut. You will never change their teaching of it.