Bumping a super old topic. Maybe I should start a new one?
I’m not sure how things were in 2016, but Google is now indexing embedded Discourse comments. You can confirm this by searching for some of the comment content from https://blog.discourse.org/. Note that Meta hasn’t enabled the embed set canonical url setting, so you may get duplicate results when searching blog comments, or you may have to click the “Show additional results” link on Google to have blog comments returned instead of just having the Meta post returned.
My concern around this is largely SEO related. Irrelevant or negative comments can hurt SEO. Relevant comments that add additional context to a blog post can help SEO: Google On The SEO Value Of User Comments On Websites.
The WP Discourse plugin deals with this by having an Only Show Moderator Liked option to control which comments are displayed. Adding a similar feature to embedded comments would be straightforward, but would it be better to have an explicit checkbox shown to staff to determine whether or not comments get displayed on a blog post?