The most forthright way would be to play around with the
post sub of lib/MT/App/Comments.pm to get it to do what you want. If the URL is right except the missing anchor (which is what it sounds like), you may merely need to change line 153 from
CODE
return $app->redirect($link_url);
to
CODE
return $app->redirect($link_url .'#'. $comment->id);
or however you have the anchor configured.
If this doesn't count because it's not easy, I guess that's a "no."