I think the risk is primarily bad press. It's not really a "security hole" for apps to add additional runnable code from an external website, when apps can currently contain pretty much anything at all (as long as they don't link to forbidden symbols). Remember that Apple does not see source code, and relies completely on app developers to behave, beyond a few perfunctory checks.
And Apple has made it abundantly clear that they don't care about bad PR in the security community. So there's really no downside to cutting out Charlie Miller, in Apple's eyes. The winner here is Charlie Miller's career.