I had a look on the payment module and it seems not so easy.
As far as I could see, the module itself doesn't process order totals, it passes the prices for each product and totals seem to be calculated at the payment page. So you would need to add the order total processing and then pass the discount amount like an additional item (product) with negative price.
Something similar is done in the paypal express module.
You chould have a look on it.
Or you could check the API of the payment provider if there is an order total discount variable available.
Anyway, not easy and not possible to give you exact instructions without having access to the payment processor for testing.
The guest orders are flagged in the cm_cs_pwa_products_purchased.php module. Please make sure you are using that content module instead of the core module in the checkout_success page.
The related code lines are:
// flag guest order
tep_db_query("update orders set customers_guest = '1' where customers_id = '" . (int)$customer_id . "'");
You also could check if the session parameter "customer_is_guest" gets correct registered during checkout process.