That's an overly pessimistic view of the situation when you consider that iOS already supports multiple devices with multiple resolutions, and MacOS X supports multiple devices with infinite resolutions. Neither are what we would call fragmented today.
The reality is that the industry has figured out long ago how to support an arbitrary number of display devices from a single operating system. It is true that it is not easy or practical to scale mobile applications arbitrarily since they are typically designed around a fixed pixel display area. But you can letterbox or pillarbox easily, and other solutions such as the one proposed in the original post with regard to scrolling apps are available as well. And just as crucially, you can let the user choose which solutions they prefer, and on a per-app basis. I might want to scale my email app and live with the possible artifacts, but choose to play a game at its native resolution with a blacked out surround. It does not have to be a big issue if you allow for some creative solutions to the problem - an approach Apple has been quite successful with.
A larger, more spacious iPhone screen is inevitable at some point in the future. It will happen. And it will all behave in a graceful way.