Looks like I had to figure this one out myself.
replace $comment_meta_args and $replies with
global $wpdb;
$comment_meta_args="SELECT * FROM `$wpdb->comments`
WHERE `comment_approved` = 1
AND `comment_parent` = (". intval($parent_comment_id) .")
AND `user_id` != 1 ORDER BY comment_date ASC LIMIT 3";
$replies=$wpdb->get_results($comment_meta_args);
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