There is no way of making Disqus work, the issue is that Disqus uses the referer to work and it can be on any website, thus when the requests go the referer is removed because it's going to the disqus domain from another domain. Unless you add all the websites that use Disqus to the whitelist of RefControl, they won't work. You should tell Disqus to fix the issue because it's nothing we or RefControl guys can do.
If it's enabled, it's working, the whole point of the addon is to be minimal and not require any fiddling other than the strict mode in case you need to use websites with weird domain setups.
EDIT: ok, I added whitelist support and tested, it now works with Disqus, check the README here: https://github.com/meh/smart-referer for what to do. Keep in mind it will take some time to be reviewed, in the meantime you can use the package in the download section of the page I posted above.