I was a little weirded out by Kira thinking she felt sorry that Taran'atar was a non-beilever, that's not quite how I remember Kira. Cenn saying it a chapter or two earlier about Ro felt abrasive but in-character.
I took it as Kira thinking more about how it must feel to lose a faith you once had, since she knows the comfort she gets from it, as opposed to just being a non-believer in general. Whereas Cenn I couldn't definitely picture thinking to himself, "There must be something wrong with those people."
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I agree. Although Kira never really lost her faith in the Prophets, she was forbidden from actively taking part in that religion. She knows what the seperation feels like. Taran'Atar does too. She can understand that.
Cenn.... I like the guy, but he's clearly more of a zealot then he'd like to admit. Almost preventing people from challenging his beliefs. And people who don't want to be challenged, might be more uncertain than they'd like to admit.