Of course they can. They own the directory server that hands out keys.
http://blog.cryptographyengineering.com/2013/06/can-apple-re...
tl;dr: Apple can send you a public key of Bob's new device. Apple can pretend to send you a public key of Bob's new device. And since it's proprietary software, they can trigger a resend of your recent messages to Bob.
Moreover, if you use iCloud backups, they have the keys to your kingdom, since it fails the 'mud puddle test':
http://arstechnica.com/security/2013/06/can-apple-read-your-...
Apple control iOS so they could just release an update that disables crypto and leaks all the messages - your point is irrelevant since they can't trigger a resend without an update to iOS.
You can reset your password and redownload all of your messages to a new device if you use iCloud backup. Cook is full of shit when he says that Apple doesn't have the capability. They own the system.
Even a dedicated civilian could reset your password, associate a device with your account and receive all messages going forward. To state that Apple cannot is such a laughable claim that it becomes clear that it's just a PR game. Which calls into question how sincere he is in his feelings about privacy.
A civilian could still associate another key (device) to the account if they're dedicated with the password or a password reset (not as stealthy) assuming 2FA is disabled. And Apple could surely do it stealthily since they own the system.
They have the capability, and it's too kind to his statement by calling it a half-truth in that respect because it's really a lie when he says "[Apple doesn't] have the capability."
How? iMessage encrypts and sends a copy of every message to every device registered to a recipient (iPads, iPhones, Macs, etc.), each of which has distinct public keys. It's actually a pretty ingenious aspect of iMessage, that it can support multiple devices without any private key exchange.
But..... those recipient public keys are provided by Apple. So in theory Apple could add itself or law enforcement as another "device" -- let's call it "fbiPad" -- completely bypassing all that security.
However the "good" news is whether Apple is actually doing that in a given instance could theoretically be detectable by analyzing network traffic, since it would result in an additional copy being sent. Even though it's encrypted you could probably tell by the amount of data.
There can never be any security on a closed system where a central party has all the control. That means apple's system is a lost cause for user security.
Also better not use a phone. Because Android and Windows Phone would have the same problem.
To bring that up in the context of iMessage security shows either ignorance or stupidity.
And remote deleting is quite a bit different to silently upgrading apps for the purpose of spying.
According to my research, Apple has NEVER used the "kill switch", unlike Google: 'Google also possesses a remote "kill switch" for Android apps, but unlike Apple, it has made use of the feature before. In 2010 the Android security team deleted two apps created by a security researcher after they "misrepresented their purpose in order to encourage user downloads." Its kill switch is referred to by the company as the "Remote Application Removal Feature.' [1]
[1] http://www.businessinsider.com/brazil-orders-apple-to-use-ip...
I can guarantee you that the "automatically add purchased content to this phone" check box does absolutely nothing to protect your phone from downloading and integrating data from Apple silently if they should choose to target you. And you would likely never know if they choose to target you.
Of course Apple can "silently slipstream applications onto a user's iPhone". Whether they'd risk getting caught doing it (even for non-all-powerful law enforcement agencies) without a court order or for anything less indefensable than a kiddie porn investigation is less clear. (And whether the NSA would even need Apples help to do it themselves is questionable - I suspect whoever owns the baseband has as much access as you'd even need, so now you're relying on AT&T/Comcast/Verizon/TMobile to put protecting your privacy above keeping the corporation on-side with powerful government agencies...)