Yes, you can easily do that with JFBConnect. In the "Social Configuration" area in the "Content Plugin - Comment" tab, you can configure how the comment box looks, and where it would be added. There's specifically a "Category Setting" where you can set specific categories to include or exclude.
With that setting, you should be able to do exactly what you're looking for, but if you have other questions, just let us know!
Alex
Comments for all articles in selected categories
