Close Magento Orders - it's a once off thing. Don't really care about repercussions.

closeOrders.php

// Instantiate Magento
define('MAGENTO_ROOT', "shop");
$mageFilename = MAGENTO_ROOT . '/app/Mage.php';
require_once $mageFilename;

umask(0);

Mage::init();
//$orderIds = array('100006363');
//
// For Below to Work, change line 652 to false temporarily ie: return $this->_setState($state, $status, $comment, $isCustomerNotified, false);
// in app/code/core/Mage/Sales/Model/Order.php

foreach($orderIds as $orderIncrementId){
    $order = Mage::getModel('sales/order')
        ->loadByIncrementId($orderIncrementId);
    $userNotification = "Closed Manually due to no stock";
    //$order->_setState(Mage_Sales_Model_Order::STATE_COMPLETE, false, '', $userNotification, null, false);
    $order->setState(Mage_Sales_Model_Order::STATE_CLOSED, $userNotification, false);
    $order->addStatusToHistory(Mage_Sales_Model_Order::STATE_CLOSED)->save();
    echo "Closed Order" . $orderIncrementId . "\n";
}