I may be out of my mind for saying this, but you could download whatever the page's code is (html, css, java etc. files) and then parse them to see if threre's an alert in it, delete the alert in the document if its there, and then have the UIWebView reread the edited document, I don't think this would be efficient though, I think it would take an awful long time just to load one web page.
So, you don't have control of the webpages that are being displayed in your app? Besides, once the user clicks the OK on the alert, the app continues, yes?