There's a difference between sites designed solely for commenting on arbitrary articles, and comments sections tacked on as an afterthought.

Have you ever seen an intelligent, multi-comment discussion in blog comments? What about here? That's the difference.

Yes, frequently, especially attached to intelligent blog posts! For instance, good, well thought-out articles linked here have insightful comments that sometimes people even point out here.

Overcoming Bias (Robin Hanson's blog) have decent discussions for a blog...

I've seen good discussions in comment threads on various political-themed blogs for my local area. One that springs to mind is the Seattle Transit Blog. They have a good (bad?) number of trolls. However, they don't tend to overwhelm the discussions about the history of regional transit policy and how it relates to municipality X's service imbalance.