The second part of the quote is “Whenever there’s a conflict, the logic of security will trump the right to privacy." The full CNBC quote that's so often partially quoted is

I think judgment matters. If you have something that you don’t want anyone to know, maybe you shouldn’t be doing it in the first place. But if you really need that kind of privacy, the reality is that search engines, including Google, do retain this information for some time. And it’s important, for example, that we are all subject in the United States to the Patriot Act. It is possible that that information could be made available to the authorities.

and at his Techonomy talk what he argued was that the only way for governments to manage the Internet was to do away with anonymity. I think he's pretty consistent; governments will invade your privacy in the name of domestic repression, and Google will help in any way it's asked. It's not changing his position to say that if you want to prevent that, you'll need to do something. Changing his position would be saying Google was going to lobby against state surveillance, or even more unlikely, refuse to comply.