Users can be deleted by running the following command:

sudo deletesftpuser <username>

This will delete any local files in the user's home directory, so make sure you make a back up first.

Note: Deleting a user will not delete the data stored on S3. However, the user could have SSE-C custom encryption keys stored in /home/username/.sftpgateway/ that may have been used to encrypt individual S3 files.