Imagine for a moment that we live in the hypothetical world where the search engines allow you to control your own privacy. Imagine we live in a world you are allowed to access search engines using SSL. A world where the search engines allowed you to prevent third party intermediaries from intercepting the content of our thoughts with the same minimum diligence used to protect our credit card numbers during an online transaction.
In such a Utopian society, search engines would go the next step and not log your search request if you accessed through their sites through that secure connection (unless they were already subject to a government SEARCH WARRANT to spy on you). Of course, to protect themselves and their advertisers against click fraud and address other legitimate concerns, the engines could still associate data for paid links that you clicked, for example, without saving the actual query or the organic clicks.
These steps are not the complete solution, but they are a small start to swinging the pendulum in the other direction.