I've tried using the function comments_popup_link, which in combination with comments_popup_script, should give a link for a popup window with the comments in it.
But the problem is, this popup loads a file from the wp default theme (wp-content/themes/default/comments-popup.php)
However, including the wp theme engine seems to be a problem.
It does'nt use the wpmu site templates and in this case loads the complete site into a popup window, so it looks a little strange ;-)