Looks like they broke it. Modify function remove() in includes/modules/payment/braintree_api.php. Replace what's there with this:

Code:
    function remove() {
        global $db;

        $db->Execute("DELETE FROM " . TABLE_CONFIGURATION . " WHERE configuration_key LIKE 'MODULE\_PAYMENT\_BRAINTREE\_%'");
        $this->notify('NOTIFY_PAYMENT_BRAINTREE_UNINSTALLED');
    }
Please report this issue to the Numinix guys. Thanks.