Cannot delete Desktop and Documents folder from iCloud Drive after accidentally enabling their storage on iCloud
From my MacBook's Finder window, I deleted the empty Desktop folder from iCloud Drive and then immediately emptied the trash before the folder had time to reappear in iCloud Drive. The folder did not reappear. 

After a few seconds iCloud refreshed and the Documents folder was deleted from my iOS device as well! 

I then followed the same steps to delete the empty Documents folder.

Cheers!