You can try to stop it in the `pre_comment_on_post` hook

 add_action('pre_comment_on_post', 'no_wp_comments');
 function no_wp_comments() {
 wp_die('No comments');
 }

I use this when I use Facebook comments instead of Wordpress comments. 

Here is a similar example with an anonymous function:

 add_action('pre_comment_on_post', create_function( '','wp_die("No comments");'));

but I prefer the first example, it's easier to modify.