I'm releasing parts for a new nodetype called discussTree.
I've been experimenting with them on Scripting News. .
The best example I have so far is citybikes.blorkmark.com
Still to-do: A template for this type. I've been using a hacked-together template.
To create one of these, set the nodetype to discussTree and save it.
When rendered, you should see a discuss symbol to the right of each line.
When you mouse over the symbol, the text should be underlined, so you can easily see which line the comments a related to.
The number to the right of the symbol is the number of comments.
It should use your Disqus settings to choose the group.
There's also a new pref on a per-root basis, that allows you to change the URL of the popup window. It points to a page on one of my servers, and you're welcome to continue using that. Or you can create your own.
AC has it working on his server.
He says: "If you use the default comments template http://disquspopup.scripting.com/ as set in prefs, you will need to enable access to this in your disqus settings by adding disquspopup.scripting.com to 'Trusted Domains'."