Actually having 'full' control over one's own hardware is pretty much impossible (and AFAIK will remain so for the foresee-able future without some major changes among the companies that make hardware and write firmware).
Apple has a varied track record on the degree to which users are allowed to have control, they do better on OSX and worse on iOS (which is a big reason I use Android and a MacBook Pro).
That said, this particular incident is an example of Apple standing up for the right of consumer to control their devices , particularly to control who has access to the data on them).
As such, it seems completely reasonable for the EFF (and the rest of us) to support Apple in this case. Failure to do so because you dislike some of Apple's other decision is cutting off the nose to spite the face
You may be missing it, yes.
As I understand it, the issue is not about software, but about the security keys. It isn't about some code being written, but about signing that code with the root certificate of all iOS devices.
Nobody is celebrating their closed-source codebase as a paragon of security. If Apple used open source code, sure the FBI could pay a third party to write the code, but Apple would still be right to refuse to sign it.
[edit: softened tone]