Sierra has disabled the "install from any source" option (although you can re-enable it with some terminal magic). How long until they disable the identified developers option too and leave a system like the iphone?
Apple is never going to completely lock down the Mac because it can't be a development platform if it is locked down. Besides, why would they even want to?
I would bring up a libertarian argument to counter this view, but unfortunately I don't politically lean that way do it wouldn't be authentic. Somebody definitely should make that point, though.
Like Richard Stallman?
Never. That would literally kill the platform. And nothing Apple has done has indicated that they even want to go this route. For example, against all expectations, they haven't been expanding the set of sandbox exemptions for apps, which means there are still large classes of apps that cannot be distributed on the App Store as they need functionality that isn't available in the sandbox.
Removing the "disable Gatekeeper" option from the UI does not indicate that Apple wants to force everybody on the App Store, it means that Apple wants everybody to codesign their apps. But, as you already mentioned, you can easily re-enable it from the CLI, and anyone who isn't capable of finding out how to do that is almost certainly not qualified to judge the security implications of making that change.
Also one of Sierra's new features is adding support for non-MAS apps to use iCloud features. If they were planning to freeze out non-MAS apps, why would they do that?