uBlock Origin – How to Block Root Site Without Blocking Sub-Pages

You can easily add Disqus in your filters.

You just add the following:

||disqus.com/embed/comments/
###disqus_thread

To add a filter, go to the uBlock Origin Options page and go to the My Filters tab. Over there you just add the lines you wanna block and click Apply Changes on top.

This answer attempts to block Hot Network Questions (HNQ) only on Stack Exchange (SE) homepage (as per OP's comment).

The HNQ on SE Homepage is inside a div with question-list ID, thus the needed filter is stackexchange.com###question-list.

This filter will only block HNQ on SE homepage. It won't block SE Realtime Questions (the parent container is main-area, which is shared with HNQ list) nor any question lists on other sites (they use div with question-mini-list ID on their homepage and questions on their Questions list)