How are you supposed to test whether or not Apple will discover a vulnerability during their AppStore approval process if you are going to tell them that one exists?
That said, this guy broke the legal agreement that we partly rely on for trusted computing in iOS. He can be thankful if he doesn't get sued, and he should have gone about it differently if not willing to face the minimal consequences of violating the legal agreement.
I personally don't really think there's anything at all wrong with a bit of harmless, nerdy limelight-seeking to boot, if that's what he was doing. Acting like he was somehow mistreated is what seems a bit iffy.
Unfortunately, I know of no other way to do it, unless companies like Apple create security groups that work with people like Charlie and give him an exemption to submit, and not notify other parties at Apple.
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.