you need to add inline style on the email template Like 

    <p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

also you can change function in this file 
    

> /app/code/core/Mage/Sales/Model/Order.php

    

    

    public function queueNewOrderEmail($forceMode = false)
    {
    ...
            
    if ($this->getCustomerIsGuest()) {
          $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
              $customerName = $this->getBillingAddress()->getName();
          } else {
          $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
              $customerName = strtoupper($this->getCustomerName());
          }
        ....
     }