Kirk McElhearn talks through the process of deleting iCloud documents from iOS and the Mac.
On the iOS side, he’s right on the money. But on the Mac side, Kirk says:
It’s surprising that you can’t do this from a Mac. But there are ways to access, and delete, files from OS X, such as by navigating to ~/Library/Mobile Documents, where you can see all your documents in a Finder window. If you delete documents there, they get deleted from iCloud in the same way, but the interface isn’t designed for you to do this.
This option is a bit tucked away, but if you go to System Preferences… and select iCloud, you’ll see a Manage… button. It’s pretty much the same interface.
I do like the mention of ~/Library/Mobile Documents, though I’d strongly suggest using the interface. Using the Finder to delete files when there is an interface designed specifically to delete them is asking for trouble.
I would also recommend logging in to iCloud.com and clicking the circled ? in the upper right corner. That will bring up an excellent help window with coverage on storage management and a host of other useful topics.