According to what I have read is that google doesn't index content from any cross domain iframe since it's the content of another website. So how does Disqus do it?
This is because what you had read is not fully true, as Google says:
Google tries to associate framed content with the page containing the frames, but we don't guarantee that we will.
Or it was before 2011, when Matt Cutts from Google said:
Googlebot keeps getting smarter. Now has the ability to execute AJAX/JS to index some dynamic comments
Disqus comments are being indexed by Google, (Facebook comments too), I have tested myself and I can find Disqus comments in SERP.
From a previous Disqus statement they said regarding iframes:
we decided to completely re-implement our commenting embed inside of an iframe. This iframe is hosted on disqus.com and, as such, the browser won't let your website apply styles to it using CSS statements. We did this for a few very important reasons:
The iframe is part of our solution to provide full indexing of Disqus comments by Google and other search engines, without having to duplicate content on your website (e.g., through a WordPress plugin).
And about Google indexing comments:
Disqus is fully indexable for search engines out- of-the-box. We have been approved by the Google Search Quality team to be organically crawled unlike any other comment platform.
So Google bot has become "intelligent" enough to realize that the iframe content are comments related to each webpage and can be indexed, they are not just displaying content from other webpage, but at the end, Google always has the last word:
While Disqus implements the necessary functionality for Google to crawl comments, indexing comments is at Google's discretion.