Apple is working hard to provide a secure and still fully functional system. Some things will break, undoubtedly. Some apps will be abandoned, either because of legitimate technical limitations Apple refuses to address, or because of political stances taken by the apps' developer. Things aren't perfect right now, and Apple still needs to continue refining and enhancing the OS X sandbox.
Is it as clear-cut as Rentzsch makes it out to be, though? Absolutely not. In fact, I think he takes a very biased stance in this article. For the vast majority of users, sandboxing is an enormous step forward for the safety and security of their data and system. For that reason alone, I encourage everyone to purchase apps via the App Store. It's a safe and trusted distribution vector that is now helping improve OS X's platform security. That's an enormous benefit to almost all consumers.
(And I say all of this as a developer who's having to wrangle with the sandbox right now.)