While I welcome getting rid of disqus, the new comment system seems a bit convoluted / disjointed. I click on the ‘Have your say’ link, and it takes me to this forum thread to add a comment here. Why not just allow adding a comment directly below the article?
This new system seems to have many of the same problems that Disqus had, though not quite as bad since the extra cruft is only loaded when you actually want to make a comment. The SEO issue is slightly different as you do now have comments on the article. But instead you now have a duplicate content issue since the article and comments are reproduced in this forum thread. (Unless you’re blocking comment threads from being indexed?)