How to maintain changes to comment-template.php

There’s a filter for that: get_comments_link. Refer to source:

return apply_filters( 'get_comments_link', $comments_link, $post_id );

In an appropriate place (such as a site functionality Plugin), just add a filter via callback:

function wpse123906_filter_comments_link( $comments_link, $post_id ) {
    // Return your custom link
    return get_permalink( $post_id ) . '#disqus_thread';
}
add_filter( 'get_comments_link', 'wpse123906_filter_comments_link', 10, 2 );