From what you've said I'm not sure you are actually aware of what Google Apps is.

http://www.google.com/enterprise/apps/business/

It's a service from Google where you get to use their applications (gmail, gdocs, gcal, gsites, gdrive, etc) under your own domain and gives you full control over the users. It is your own private instance of Google's products that you have control over.

Now, for small groups (I think ~10 users) you can get a free instance of Google Apps setup where they will collect data like they do with their other free services that you normally access. But they could not offer this service to Government organizations if they were collecting any data from the service. As long as you pay money for the service you have control over Google's data collection for your private instance of Google's services.

Now, I just read over the privacy policy for Google Fiber and it states that they will not assign any information regarding websites you visit to your identity. They of course will know what sites their entire customer base visits because that information is actually critical to ensuring the network is running smoothly (what's that? Can't access yahoo.com? Lets check the logs. Yup, at 12:00 yahoo stopped responding for all users in region Y which corresponds with update X, etc etc) and is something that every single ISP does. And since it's not being associated with any person but just the faceless blob of all their customers you as an individual are protected.