You can do this using install which is update this free shipping method details using
$groups=array();
$groups[freeshipping][fields][active][value]=true;
$groups[freeshipping][fields][free_shipping_subtotal][value]=0
here [freeshipping][fields][active][value]
is field name .you can see this in
here freeshipping
is shipping method
code and active
is field name of activation
from admin input field
Mage::getModel('adminhtml/config_data')
->setSection('carriers')
->setWebsite(null)
->setStore($StoreId)
->setGroups($groups)
->save();
if you have multi store then you need fetch all store and run this code in foop
see more at
https://stackoverflow.com/questions/2474039/magento-update-store-logo-programmatically