I think they're riding it out. Cook is nowhere to be seen because he isn't likeable, which is why they sent Federighi to do an interview. That was Cook's job. They are looking for the least amount of interaction in hopes this blows over, which it probably will. I think the more they come out and fight this, the more chance it has of reaching mainstream media where regular people who aren't on MacRumours will read about it. So Apple does little and for the most part doesn't want to fan the flames. That's what it looks like to me.
Either that or they are being forced to do this and they can't or won't admit to it.
It is, in my view at least, because now the "What's on your iPhone stays on your iPhone" is "What's on your iPhone, stays on your iPhone, except..." and that last part is the problem. I don't necessarily think this particular technology is the actual problem, though it could be. I view this as a slippery slope and a problem in two ways: 1. Apple did something they never even suggested they would do and I for one never thought they'd do it, 2. it creates a psychological shift. If this is accepted, which it most likely will be by a majority of users, the next time Apple is covertly forced into something else, it won't be as shocking. It will be the same stuff, just about a different topic. See how people react to privacy violations in China - they all use WeChat, everyone can be under surveillance so who cares. That's the slippery slope, it's not just the prospect of abusing this technology (let's even say that cannot happen), but the idea, which will become normal, that Apple installs spyware/surveillance software/whatever you want to call it on the iPhone. Until now, unheard of. Next year, business as usual, only they'll scan for something else maybe.