From what we can see in the release notes of the new JSS version, there is no possibility to prevent a Mac with Sierra from syncing files from Desktop and Documents into iCloud. Does anyone know how to prevent that? We don't want our bandwidth clogged and users confused with the "low iCloud storage space" messages.
Great question @St0rMl0rD. At this time, Apple does not provide any configuration profiles to limit this new macOS Sierra iCloud functionality. I would recommend filing a request with them to add this feature.
Apple has announced their intention to allow for skipping the set up of iCloud Desktop during DEP enrollment, however it is unclear whether this will wholly remove the feature for DEP users or whether it will simply not prompt them at setup. Once Apple releases documentation to support skipping that step during DEP enrollment, we will add it to the product.
I hope that helps!