I’m having the same conflict on my own wordpress website (www.froyok.fr/blog).
I had to disable social plugin to get back the disqus comments. Otherwise I get the message “Comment are closed” AND the classic wordpress comments (which by the way don’t take in account my own theme).
We discovered this problem as well, after having comments effectively disabled on our site for 18 hours.
On the Social settings page, there’s an Advanced Options. Click it and it’ll expand. Then check the box that says: “Disable Social’s comment display (use standard theme output instead).“
That should allow Disqus to appear again if it worked before. Social hijacks the commenting section and that’s why it conflicts with Disqus. Of course, Disqus hijacks too, just in a different way while Social hooks itself in earlier. Hope this helps.