Вы пробовали VbScriptMsgBoxDialogHandler? По примеру
var handler = new VbScriptMsgBoxDialogHandler(buttonToPush);
using(new UseDialogOnce(Ie.DialogWatcher, handler ))
{
Ie.Button("vbScriptMsgBox").ClickNoWait();
handler.WaitUntilHandled(10);
Assert.That(handler.HasHandledDialog, "Should have handled dialog");
}