I think the practice of chewing apart someone's religion is pretty emotionally trying and leaves the person feeling like the community hates their entire being/identity,

Yes, it would be. In my experience, I haven't felt that my religion has been chewed apart; by and large, most people on the site seem to shrug and ignore it. So this situation hasn't yet turned up here for me.

Though you are right; such a sentiment would go a long way towards repairing emotional damage. Actively pointing out and encouraging behaviour that you like is a good way to get people to behave that way more often. I think that's most of the reason for the karma system; to upvote posts encourages similar behaviour in the future. Replying, with specific reasons for an upvote, encourages a more specific behaviour (and upvoting the encouraging post will probably reinforce the enouragement).

In person, I'm told that eye contact and attentive listening work surprisingly well.