Wasn't it just yesterday a story was published about an upcoming documentary about the STUXnet virus that claims that the US and Israel developed it in secret together and had a very successful, but very limited use for it. Only when Israel allegedly went off on their own to modify and deploy it did it spread wide and far, popping up on the radar of anti-malware companies and getting researched and publicized.

Like what you said, after the exploit/backdoor/software is designed, it can never be un-designed. It will exist as a tool that can only be mitigated, but not destroyed.

Then why don't we have Apple's private keys yet?

Plenty of companies keep a lot of things very secret, including things like powerful debug modes, for a long time. At least long enough that everybody forgets the details and the software has long since rotted away.