I did this by writing a little method to handle it, don't know if it is the right way, but it works.

private static void UpdateLocale(string en)
    {
        XmlDocument languageFile = XmlHelper.OpenAsXmlDocument(en);
        XmlNode rootNode = languageFile.SelectSingleNode("//area[@alias='sections']");
        if (rootNode.SelectNodes("key[@alias='aliasValue']").Count == 0)
        {
            XmlNode newNode = (XmlNode)languageFile.CreateElement("key");
            newNode.Attributes.Append(XmlHelper.AddAttribute(languageFile, "alias", "aliasValue"));
            newNode.InnerText = "Nice String";
            rootNode.AppendChild(newNode);
            languageFile.Save(System.Web.HttpContext.Current.Server.MapPath(en));
        }
    }

This is called like this UpdateLocale("/umbraco/Config/Lang/en.xml");