Also better not use a phone. Because Android and Windows Phone would have the same problem.
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...)
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.