"Hi, darling. I've decided to worship demons. You are okay with that, right?"
"No."
I'm not sure that qualifies as intolerance. If you aren't in a relationship, she just says "fine, whatever, we'll just agree to disagree. Let's deal with Corypheus." She's fine with leaving you to yourself if that's what you want. She's not fine with having a relationship with someone who thinks her faith is a lie.
Because you do realize that she's right, don't you? There's no way the Creators can be "Divine" and the faith of the Maker be true. If you say that worshiping a fade spirit is cool, you inherently saying that the Maker's faith is false.
Now I can see how the dialogue there could be intended to be more equivocal in the player's mind, but its pretty clear that its written as if the inquisitor is saying "what if Mythal really is a god?" rather than just "obviously there was something there and maybe it wasn't a demon, even if it wasn't a god." I know I was a bit caught off guard by that interpretation of the line when I played it.