I'm not familiar with pure-ftpd, but the setting you're looking for is the default 'mask' that the server applies to incoming files.
If the server doesn't have options to support this, you could always write a cron job to set the permissions on the directories correctly at a given interval (or get an FTPd that does).
scp and rsync are just a couple of examples of uploading files to a site without employing FTP
