How can I upload a directory structure from a PC to iCloud without first copying it to my iCloud drive?
As of macOS Sierra 10.12.5 (and the equivalent iCloud for Windows), iCloud Drive does not offer a facility for selective-sync of files between your local storage and the cloud.

Therefore, anything you upload to iCloud Drive using the web interface would then make its way back down to your local storage on any machine logged in to iCloud.

iCloud Drive doesn’t appear to be the archival storage solution you’re looking for. It’s a full-syncing service.