Magento How do I enable free shipping in backend only (for order entry)

1> Override or your custom shipping method file 

     app/code/core/Mage/Shipping/Model/Carrier/Freeshipping.php

      or 
     app/code/local/YourCompany/NewModule/Model/Carrier/ShippingMethod.php

2> You can find 

   public function collectRates(Mage_Shipping_Model_Rate_Request $request)

  And add below two code in function 

        if (!Mage::app()->getStore()->isAdmin())) {
            return false;
        }

     after below these two lines

        if (!$this->getConfigFlag('active')) {
            return false;
        }

And set to active in backend

You can place the code in local if you dont want to overwrite the core

This should work