Check out the role architecture diagram at http://blogs.msdn.com/b/kwill/archive/2011/05/05/windows-azure-role-architecture.aspx. You can see that the startup tasks are executed before IISConfigurator creates the application pool for your website. This means that the only place you can make modifications to the apppool is in OnStart.
I haven't tried this, but you could create a background type startup task which will let the rest of the startup process (ie. running IISConfigurator) proceed while your startup task is still running, and then within that startup just loop until the virtual directory is detected.