I'm sure they will still have a compiler on the system -- it has to be possible to compile code for this machine from source and run it ...
As I think about it -- wouldn't app store (if well run, then it provides the best possible security for distribution of binaries without source code and the most consumer friendly commercial licensing model) + open source eco-system (self-compiled -- source only distribution) pretty much the best possible world for users? There is (kind of) an open-source argument for making binary distribution without source onerous or impossible...
Perhaps they'll bundle or distribute an official version of something like homebrew to make installing open-source software as easy as possible and maybe even provide a way for binaries generated from these packages to become signed and distributed as binaries as an optimization?
I don't think I would mind app-store being the only way to get pre-compiled binaries if augmented with a well-supported open-source ecosystem for utilities that need to venture beyond the capabilities of the app-store sandbox. There is a technical argument for making any software that needs to operate beyond the sandbox subject to source code auditing simply because of the potential attack surface ... I wouldn't necessarily mind if subscription pricing was the only business model for such sandbox-spanning utilities -- continuance maintenance (and ongoing revenue) for software that works beyond the sandbox is needed from a security perspective ...