This will make posts get queried in order by the term_order defined for the post in the term_relationships table

order-posts-in-term-by-term-order

function my_order_posts_in_term_by_term_order( $orderby, $query ) {
	global $wpdb;
	return "$wpdb->term_relationships.term_order ASC";
}
add_filter( 'posts_orderby', 'my_order_posts_in_term_by_term_order', 10, 2 );