Stack Exchange has several religion sites and they all have faced this problem to one degree or another. In particular, I'd like to direct your attention to What Christianity.StackExchange is (and more importantly, what it isn't):
I've come to understand what is and isn't acceptable in a way that can be expressed in two images.
In one, I picture a seeker, maybe coming to their Pastor or Priest, or maybe climbing a mountain to ask a guru the secret of life, or hoping the heavens will open up and divinely reveal absolute truth.
In the second picture, I see a giant person peering into a box with a magnifying glass, viewing all the little Christians running around with their various beliefs, saying "Oh, hey, look at this. That bunch over there believes in predestination while these ones over here don't. I wonder why that is. Hey, little guy: Why doesn't your group believe in predestination?" The little guy answers, and maybe triggers another little guy to ask a question of another, and sooner or later, all understand each other just a little bit better.
This site is more like that second picture.
One thing that has worked well on the Christianity site is a series of tags for specific denominations/sects. These are (more or less) required on questions where the accepted answer varies from one Christian group to another. In this manner, questions are about facts and not absolute truth. The Judaism site tends to be a little more narrow, which means diversity of opinion is handled on the answer, rather than question, level. Islam has developed wide-ranging policies and questions can be either general or directed to specific sects.
I don't know enough about Hinduism to know which approach will work best, but be aware that users are expected to adopt a respectful attitude toward beliefs they disagree with. There's no room for pronouncing absolute truths.
See also: Why Sectarianism is Ruining Your Site.