The previous Disqus added the content of the commenting system into the page's DOM, which allowed overriding and adjusting the CSS.

Update: Disqus' RTL support is implemented now

Since this web site is bilingual, the other language being Hebrew, I've used CSS to properly lay out the elements for Right-to-left (RTL). Here's the lesscss excerpt I've used:

html[dir=rtl] {
  #dsq-content ul, #dsq-content li, #dsq-content ol, #dsq-content cite,
  #dsq-content div, #dsq-content table, #dsq-content td, #dsq-content th,
  #dsq-content p, #dsq-content a, #dsq-content img, #dsq-content caption {
    text-align: right; }
  #dsq-content {
    .dsq-options span { margin-right: 0; margin-left: 10px; }
    .dsq-request-user-logout { float: left; }
    .dsq-request-user-name { padding: 0.25em 0.5em 0 0; vertical-align: top; direction:ltr }
    .dsq-post-footer .dsq-button { float: left; margin-right: 3px; margin-left:0;}
    .dsq-attach-media { float: right;}
    @dsq-margin: 30px;
    .dsq-comment { margin-left:0;}
    .dsq-depth-1 { margin-left:0 !important; margin-right: @dsq-margin;  }
    .dsq-depth-2 { margin-left:0 !important; margin-right: @dsq-margin * 2;  }
    .dsq-depth-3 { margin-left:0 !important; margin-right: @dsq-margin * 3;  }
    .dsq-depth-4 { margin-left:0 !important; margin-right: @dsq-margin * 4;  }

    .dsq-comment-hide-thread, .dsq-comment-show-thread {
      left:0; right: auto; text-indent: 0;
    }
  }
}

But that's all gone with the new Disqus - iframe is used now, which prevents usage of the above technique.

Contacting Disqus' support regarding the issue, and the response I've got is:

"there is no concrete timeline for when this feature will be available"

I've offered my help, since I have the domain knowledge and helped other projects in the past with RTL issues, but got a response saying they are aware of it, will look into the possibility of addding RTL support, and will be in touch if an opportunity for collaboration arises.

I'm on Disqus' Transifex Hebrew team, but I see no point in helping with translations as long as the layout is wrong.