I'm pretty sure IIS will want to block programmatic reading of web.config. But if you can figure out a way around that, you might be able to read web.config and create a new web.config and user.config in a writable location (say under /Data). Then you'd need to provide instructions for someone to manually copy those files over the versions in the web root using another tool like FTP or Windows Explorer. I recommend you put every setting you can into user.config to make future upgrades easier.
Jamie