Seems to me that everything up to (and including) the initial ban was relatively sensible. You don't need absolute proof that the two accounts really are linked, it's reasonable enough to see something that indicates they likely are and then take action based on that.

Where it fell apart was failing to account for the possibility that they got it wrong. They should have notified both accounts and explained why both were being banned for the actions of one, then allowed a way to demonstrate than the two weren't really linked in order to reinstate the other account.

Unfortunately, this is pretty typical for how Apple operates the App Store. "We're never wrong, get lost" seems to be their motto. For example, for a long time you couldn't even appeal when your app was rejected. If it was rejected incorrectly, then all you could do is try to submit again and hope you got a different reviewer that time.

The App Store is a direct descendant of the iTunes Music Store, which originally existed to serve a handful of big music publishers. In many ways, it hasn't adapted well to serving a million small developers.