WordPress function/action to exclude comment type in comment count.

gistfile1.php

<?php

/**
 * Update comment count
 * 
 * @see https://github.com/WordPress/WordPress/blob/3.6/wp-includes/comment.php#L1620
 */
function prefix_update_comment_count( $post_id ) {
	global $wpdb;
	
	$new = (int) $wpdb->get_var( $wpdb->prepare( "
		SELECT
			COUNT(*)
		FROM
			$wpdb->comments
		WHERE
			comment_post_ID = %d
				AND
			comment_approved = '1'
				AND
			comment_type != 'pronamic_like'
		", $post_id
	) );

	$wpdb->update( $wpdb->posts, array( 'comment_count' => $new ), array( 'ID' => $post_id ) );
}

add_action( 'wp_update_comment_count', 'prefix_update_comment_count' );