I think this is of endgame for network security, I don't see a way out -- the Sony Rootkit[1] should have been the point where I realized but it is just sinking in for me now since the Snowden NSA leak.
Any network connected computer will be running an OS+Applications which are typically a gigabyte or more. This is produced by companies which are beholden to a nation state, and the companies can be coerced[2] or compelled[3] to use the software against the user. The software is also constantly being probed for vulnerabilities, which can also be exploited by law-enforcement / military [4][5].
So, if you turn on auto-update you have to trust the software maker is not being coerced by someone, or being compelled by a secret court to trojan you. If you don't turn on auto-update you can still get trojaned by any vulnerability. Lose-Lose.
Nobody ever cares about this stuff until it is way too late.