My opinion, for what it's worth,
Having worked extensively in Mental Health I don't get the big religion/sex connection in the song, certainly not as a big theme anyway. There are references, yes, but to me it's a song about schizophrenia, which often has an obsessive religious element to it. I see lots of "typical" schizophrenic ideas here. I read on the net a long dissection of this song talking about religion all the way through and I found it hilarious really. I think the writer had issues of his own.
I've always taken the first line to be the "mother" figure talking to a child/adolescent, telling him not to stare at his father who has mental illness. The father (in my interpretation) kills himself, leaving the boy alone with his mother. The boy develops mental health issues (fairly standard schizophrenic symptoms)- there's an ongoing dialogue with the voices- his psychosis.
Not saying it's right but that's how I see it. JP at his best though. I think it's a similar approach as 6DOIT where JP allegedly rewrote a medical textbook in lyric form- this seems based on psychotic case studies and lyric-ised. It's done well though.