And for an easy way to inject that magic line of javascript, read how to inject javascript into webbrowser control.
Or just use this complete code:
private void InjectAlertBlocker() {
HtmlElement head = webBrowser1.Document.GetElementsByTagName("head")[0];
HtmlElement scriptEl = webBrowser1.Document.CreateElement("script");
string alertBlocker = "window.alert = function () { }";
scriptEl.SetAttribute("text", alertBlocker);
head.AppendChild(scriptEl);
}