I would add

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.

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 has a URL removal tool, too, but I have never tried using it with patterns before.