That's why i feel its best not to give any karma for submissions at all. karma only for comments.
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.
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.