Hi Gill
If it's any consolation at all, when my daughter was 16/17 she asked her mum and I if we would sign a form for social services to the effect that we were irreconcileably distanced from her so that she could leave home and get housing benefit to live in a flat. We were quite upset and angry and told her that no, we weren't distanced, she wa just a teenager who at times was a pain in the ass!
Now (she is 23) we can laugh at it (even though her mum is now my ex, we are still good friends) and she agrees she was a bit daft and trying it on. (She also remembers with some humour how she had met the love of her life and decided she wanted to spend the night with him. So we talked about it, and her mum bought candles and things, her mum and I went out for the night and stayed in a hotel so daughter could have her 'first' in comfort rather than squalor, the back of a car, etc. Daughter now thinks (as do we) that this guy was a dork).
You do the best for your kids, and all you can do is hope it turns out OK.
Only you and your hubby know your son, but IME, I wouldn't worry too much about giving him the 'conform or you're out' option. He is old enough and I don't think there's too much risk you will lose him for ever. When he's just a little older he may well realise that his behaviour is not that well thought out.
As for his JW upbringing, I never was so I can't comment. But it seems to me that if he had love, a home etc. he doesn't have much to complain about. Better parents who care enough to set rules which in hindsight seem a bit wacky than parents who don't care enough to set any at all.