The article doesn't mention the updates to iOS 6, in dev hands for months, that allow for flexible layouts. I'd be surprised if any major 3rd party apps (Facebook Netflix Kindle Dropbox Spotify) weren't ready at launch. We'll see for games.
But, really, iOS has survived far bigger transitions.
I owned the first retina iPhone (4) at launch and apps were upgraded so quickly that I can barely remember using non-retina apps on it.
Many early iPad adopters ran at least some upscaled iPhone apps on it for months while developers caught up to a vastly different medium - a hideous compromise compared to letterboxing. Was that even a speedbump on the iPad's rise to blockbuster status?
So this strikes me as completely academic.