It sounds like a lot of overhead, but it's really quite simple. Objective-C is a bit verbose for a Hacker News comment, so I put it up as a Github Gist: https://gist.github.com/3080870

As for making a Settings bundle, that's pretty easy too and you wouldn't have to do it unless you wanted an easy way to let someone change their preference later.

Besides all that, I think everyone agrees with you that Apple should make it possible to do it at a system level. The simplest way to do this in my opinion would be to allow users to remove pre-installed apps if there is an alternative on the device. For instance, if I have an app that responds to "http:// URLs, allow Safari to be removed.