[SalesForce] Prevent Salesforce users from “seeing one another”

From the page you cited:

When Salesforce turns on profile-based rollout of Chatter for your organization, the Enable Chatter permission is added to all of your existing user profiles and permissions sets. This permission is automatically enabled for all standard profiles. It is also automatically enabled for all custom profiles, if any of the following user-level permissions were already enabled, either manually or as part of a license:

• “Create and Own New Chatter Groups” (ChatterOwnGroups)
• “Create and Share Links to Chatter Files” (ChatterFileLink)
• “Invite Customers To Chatter” (ChatterInviteExternalUsers)
• “Manage Chatter Messages” (ManageChatterMessages)
• “Moderate Chatter” (ModerateChatter)
• “Moderate Chatter Feeds” (ModerateNetworkFeeds)
• “Use Case Feed” (ViewCaseInteraction)
• “View All Data” (ViewAllData)

ChatterEnabledforUser will be enabled by Salesforce in the Profile of ALL Users who have any of the permissions enabled on the list above for them as part of a Standard or Custom Profile. As such, the additional permissions you're querying for are not necessary if you're trying to establish a baseline of who can access Chatter. This permission is added to ALL of your Standard profiles, Custom Profiles that contained one of the above permissions, and ALL permission sets when Salesforce turns on Chatter for you.

I'd think you'd want to know whether Chatter is enabled through a Profile as opposed to sharing through a permissionset. Consequently, I would add ProfileId to your query. Since it sounds as though you're a profile based Org as opposed to using groups and permission sets, you could create another query on User to select Id, Name where ProfileId in: list of ProfileId's returned in permission query. You could also try building your query starting from User rather than from permissionsets. That might make it easier to get a single result based on profiles along with any permissionsets you may have.

Yes this is possible, but as discussed in the comments only with this feature

http://docs.releasenotes.salesforce.com/en-us/spring14/release-notes/rn_chatter_pbr_pilot.htm

It must be enabled by support and therefore you have to log a ticket and answer some questions.

Once activated I can confirm that it worked for me as expected on two different Orgs. Also I had no negative side effects and I think you can use it without concerns.