Not possible: the global Safari cookie cache isn't accessible to third-party applications, as that would be a significant security hole. If you need to send cookie information to Safari you'd be better served launching a URL into Safari with the cookie details as request parameters and then having the script at the end of that URL create the cookies and send them back.
EDIT: If you want to be slick you can register a URL handler for your iOS app and then launch the URL to your web app. Have your web app set the cookies, then redirect back to the app URL.