I would try adding
    
    RewriteCond %{HTTP_USER_AGENT} ^Googlebot
    RewriteRule ^comment/reply/$ - [G,L]
    RewriteRule ^comment/reply/(.*) - [G,L]

to `.htaccess` or Apache config to inform spiders that the links should be removed.  Just make sure to put it before the catch-all rule at the bottom of the standard Drupal `.htaccess`.  The problem is coming up with a list of spiders to add as `[OR]` conditions to the `RewriteCond` so that they get a 410 but Drupal handles normal requests.

[Google Webmaster Tools][1] has a URL removal tool, too, but I have never tried using it with patterns before.

[1]: http://www.google.com/webmasters/tools/