unfortunately there is note 'code-related' way of enabling a specific method similar to the method applied for payment methods. Not that straight at least.
Here is what you can do:
Option 1 : No code approach
The Free shipping method can be enabled/disabled at website level.
So you can enable it on the the default config values and disable it for each website you have.
I'm not 100% sure this method works...
Option 2: Code required
each shipping method model has a method called collectRates
that checks if the method is active.
For free shipping the verification is done like this:
if (!$this->getConfigFlag('active')) {
return false;
}
You can make it not return false in case you are on the admin store view (creating an order from admin).
if (!$this->getConfigFlag('active') && Mage::app()->getStore()->getId() != 0) {
return false;
}
Option 3: Long shot
You can enable the free shipping method but make it available only when the order subtotal is over an outrageous value like 9999999.
Then create a coupon code that only makes free shipping available.
Use that coupon when creating an order from the backend.