I found this rather easy to accomplish. In your theme folder find "comments.php" and open it in a text editor.
Find this code:
<?php else : // comments are closed ?>
<!-- If comments are closed. -->
<div class="Post">
<div class="Post-tl"></div>
<div class="Post-tr"><div></div></div>
<div class="Post-bl"><div></div></div>
<div class="Post-br"><div></div></div>
<div class="Post-tc"><div></div></div>
<div class="Post-bc"><div></div></div>
<div class="Post-cl"><div></div></div>
<div class="Post-cr"><div></div></div>
<div class="Post-cc"></div>
<div class="Post-body">
<div class="Post-inner article">
<div class="PostContent">
<p class="nocomments"><?php _e('Comments are closed.', 'kubrick'); ?></p>
</div>
<div class="cleared"></div>
</div>
</div>
From "div class post" on down, delete everything and save. This will remove the message about comments being closed as well as the box that it shows up in.
... of course, not everyone's comments.php file will look the same, but hopefully you get the gist of it.