As part of my pre-release testing of macOS Sierra, I tested iCloud Desktop and Documents syncing and decided I was not going to use it because of the problems I found. However, at that time I could not find a way to disable only iCloud Desktop and Documents without having to disable iCloud Drive entirely.
As part of the release of macOS 10.12.4, Apple has made available a profile option that allows for the specific disabling of iCloud Desktop and Documents syncing without needing to block iCloud Drive.
For more details, see below the jump.
For those who want to disable iCloud Desktop and Documents, I’ve created a .mobileconfig file and posted it here on Github:
https://github.com/rtrouton/profiles/tree/master/DisableiCloudDesktopandDocuments
Once installed, you should be able to have iCloud Drive enabled in your iCloud settings.
When you click the Options… button for iCloud Drive, the Desktop & Documents Folders setting should appear as grayed out and not selectable.