I’m also looking for a solution to this. In facebook.php I found this line:
add_filter( 'the_content', array( 'Facebook_Comments', 'the_content_comments_box' ), $priority );
I tried changing it to this:
add_filter( 'comments_template', array( 'Facebook_Comments', 'the_content_comments_box' ), $priority );
But unfortunately it didn’t work. I don’t know if ‘comments_template’ is the wrong filter hook or if there is some other conditional in the plugin code to prevent it from being displayed elsewhere.