Everyone's focusing on this switch, but the switch isn't the real issue. As many have pointed out, there's no reason Apple wouldn't want to leave it around indefinitely.
If I were a Mac developer with a skepticism about Apple's increasingly tight grip on their platform, I'd be much more concerned about the widening circle of APIs that are unavailable to non-App Store apps.
You're right that the rise of Mac App Store-only APIs is more troubling. This is a "boil the frog slowly" trick. Today, you can run all the unapproved software you want, but, someday, if Apple makes the APIs compelling enough, you won't want to.
That being said, it isn't like the switch (and its parameters) and the development of Mac App Store-only APIs can't be trends that reinforce each other, of course.
Is this just iCloud, or something else? Needing to be in the app store (or signed) to use iCloud makes perfect sense to me. If you don't want to do that, simply use Dropbox -- which works better anyway (at the moment).
If I were a Mac developer with a skepticism about Apple's increasingly tight grip on their platform, I'd be much more concerned about the widening circle of APIs that are unavailable to non-App Store apps.