For me, whether I could stay with someone would depend on whether I thought their beliefs were a) due to them being bad, mean, stupid, or pretending in order to fit in, or b) whether they were a good person who genuinely believed their approach was the right one.
It very much sounds like your wife is in the b) category and she sounds like a genuinely good person. For me, this would be enough for me to stay with someone, if we agreed on most other important issues and values in life.
I hope this doesn't come across as rude as I love this board and have learned so much here - but I would be wary about using this board as your only source of advice on your relationship. I say this because for many people on here this is the ONE key issue right now and they wouldn't be able to get past it. Whereas in real life, there are many good, kind, intelligent people who fall on both sides of this argument, or somewhere in the middle (which is probably where I am). I have plenty of friends who are lovely, clever and excellent critical thinkers, who are definitely more on your wife's side on this issue.
That said, I can see that it is very hard to find neutral places to discuss this, and I worry about your counsellor not being neutral. I hope counselling will at least give you some good tools for agreeing to disagree! You can always carry on venting/discussing on here, if it's something you can't do at home!
Personally from what you say I think it would be a great shame for your relationship to end over this, but I wish you the best of luck either way.