There are two types of articles that belong here on HN. The first type includes articles that speak for themselves. Everyone learns from them, but fell little need to comment unless they have something small to chime in. This type should have a low ratio of comments to upvotes.
However, the other type includes articles that provoke people and cause discussion. It doesn't just include contributing comments, but rather it contains debates and opposing opinions. These types of articles need a balance between a low and high ratio. However, the religious arguments you speak of are usually easy to find. These arguments are usually found in a deeply nested comment thread. Once you discard of fourth level comments and all the noise below, you should find that the ratio of comments is a pretty good signifier of the quality of the article.
It's very rare that there is a huge volume (>100 comments) of insight provoked by a single article, just because there's not usually that much insight to be had in the first place on that topic, and you can be sure that 100 separate comments didn't have it all on the same thread.
You usually can only get that much noise on a topic by poking people such that they NEED to correct some injustice done by the article. Sometimes good articles poke people like this, but in either case the comment thread ends up sucking.
I second this. It baffles me when I see an article with 100+ karma and 5 comments. How can something be so interesting and yet spawn so little discussion? It makes no sense.
As pg says, those are usually very good articles. I'd say the first impetus to comment is to correct, the second to add relevant detail. When the article doesn't need either, it's good.