I think you would use:
config:
websites/{website_code}/carriers/freeshipping/active: 1
However, the config fixtures seem to have unwanted side effects like removing other config nodes.. So as inelegant as it is, I use:
public function setUp() {
Mage::app()->getStore(0)
->setConfig('carriers/freeshipping/active', 1);
// OR
Mage::getConfig()->setNode('websites/{$code}/carriers/freeshipping/active' 1);
}