Magento – Magento what is due amount, when it is generated or is it admin setting

You have to load the quote first:

<?php
    $quote = Mage::getModel('checkout/session')->getQuote();
    $quoteData = $quote->getData();
    $grandTotal = $quoteData['grand_total'];
?>

Then simply replace $this->getSubtotal() with $grandTotal.

To get the actual discount amount, you can use this:

$discountTotal = 0;
foreach ($quote->getAllItems() as $item){
    $discountTotal += $item->getDiscountAmount();
}

Until payment is received, your order will always be in a "new" state therefore the balance due will be the order total until the order is invoiced.

Try

if($validated) {
    $order = Mage::getModel('sales/order')->loadByIncrementId($orderId);
    $order->addStatusHistoryComment("Payment reference id ".$response['refId'], false);
    $order->sendNewOrderEmail();
    $order->setEmailSent(true);

    $invoice = $order->prepareInvoice();

    if($invoice->getTotalQty()){
        $invoice->setRequestedCaptureCase(Mage_Sales_Model_Order_Invoice::CAPTURE_OFFLINE);
        //$invoice->getOrder()->setCustomerNoteNotify(false);
        $invoice->register();
        Mage::getModel('core/resource_transaction')
                ->addObject($invoice)
                ->addObject($invoice->getOrder())
                ->save();

        $invoice->sendEmail(false); 

    }

    $order->setState(Mage_Sales_Model_Order::STATE_PROCESSING, true, 'Gateway has authorized the payment. Payment reference id '.$response['refId']);
    $order->save();
}