Jason,
In the Social configuration area of JFBConnect, there are two tabs: Content Plugin -Comments and Content Plugin -Likes. In each of these areas you can specify what articles (or sections) of your site the Likes and Comments should automatically appear on. In this section, simply set "Front-page" to Hide as well as any other areas you want to disable the comment and like boxes.
Hope that helps, but if you need more info, just let us know!