While I don't know what happened with your sites, I just activated the "new" Disqus on my two sites. There are four settings you can choose for this:
(1) Comments only
(2) Comments and links only on your site
(3) Comments, links on your site and 'recommended' links
(4) Same as (3) but links may be above comment box
The default setting appears to be (2); I tried this under two different Disqus accounts with three web sites, and that was the setting "Discovery" came up with each time. This doesn't strike me as particularly outrageous -- the links they are inserting are only links to your own articles, not advertising (and not revenue-generating, of course).
(1) Comments only (2) Comments and links only on your site (3) Comments, links on your site and 'recommended' links (4) Same as (3) but links may be above comment box
The default setting appears to be (2); I tried this under two different Disqus accounts with three web sites, and that was the setting "Discovery" came up with each time. This doesn't strike me as particularly outrageous -- the links they are inserting are only links to your own articles, not advertising (and not revenue-generating, of course).