The conclusion is that freedom (that is: negative, not positive rights) is the main force of progress (societal, technological, scientific). Of course, we have law enforcement, and judges, and lawyers, and an entire legal machinery: but it functions within well-defined boundaries. In the US, we have warrants. We have habeas corpus. We have chain of custody, and so on.
Apple is fundamentally circumventing these norms. And this is wrong, no matter what is on the other side of the equation. I'm not sure what Stamos' counter-argument is here. I don't always agree with the EFF, but I think in this case, they're right on the money.