The idea behind the SEO Facebook Comments is exaclty that.
Google and other search engines can't index the comments that are shown in Facebook Comments plugin because it is in an iFrame (that mean the comments are actually on another site, facebook in this case). This plugin get this comments and replicate it on the WordPress Comments database, allowing wordpress to show the comments correctly in the post and allowing it to be indexed.
If, however, you don't wan't any comment to be show and just the plugin you can edit the file on which the comment is shown, remove the function that is calling the comments (normally is the function comment_template()) and add the following line.
This method is available in version 1.5.1+ of the SEO Facebook Comments