I still don't get what the issue is; intolerance between religions, leaving aside moral questions, has been not only supremely common on the world scene for the last 4000 years, but also supremely influential. The Crusades, the Israel-Palestine conflict, hell, even the War on Terror. And that's just talking about screwing up the Middle East, there are many more examples. It's not disrespectful to faith, it's being faithful to history.
That said, the Religious Intolerance policies effects on the game as stated so far sound really boring, and wouldn't tempt me to take that terrible policy. Personally, I just see it as a speedbump to getting to Reformation. A policy which helps with cultural production would do wonders for this policy tree; perhaps adding a flat culture amount every time a foreign missionary spreads their ideas in your land (Or you in their land)? That seems pretty tolerant and it makes sense, with all the new ideas being introduced, your nation is becoming much more culturally vibrant. It's still pretty awful, but a flat culture bonus from Shrines is already part of Ancestor Worship, and it provides a continual, tangible use for missionaries beyond the Founder belief.
That said, the Religious Intolerance policies effects on the game as stated so far sound really boring, and wouldn't tempt me to take that terrible policy. Personally, I just see it as a speedbump to getting to Reformation. A policy which helps with cultural production would do wonders for this policy tree; perhaps adding a flat culture amount every time a foreign missionary spreads their ideas in your land (Or you in their land)? That seems pretty tolerant and it makes sense, with all the new ideas being introduced, your nation is becoming much more culturally vibrant. It's still pretty awful, but a flat culture bonus from Shrines is already part of Ancestor Worship, and it provides a continual, tangible use for missionaries beyond the Founder belief.