Programmatically enabled a payment method in commerce
A payment method is just a generated rule, so by enabling the respective rule, the Payment method is becoming enabled.
/**
* Enable the "paypal_ec" Payment method method.
*/
function HOOK_update_7001() {
$method_id = 'paypal_ec';
if ($rules_config = rules_config_load('commerce_payment_' . $method_id)) {
$rules_config->active = TRUE;
$rules_config->save();
}
}