You should really setup an FTP site that requires more than just a password. You can specify ident@ip + password for each account, and also set it to use AUTH TLS for added security.
If you do setup an FTPd, you could also put it in an encrypted hidden container on the server, so even the sys admins (...or anyone, y'know, "seizing" your box) would have no idea it's there, and even if they found it, everything inside it is encrypted.
Also maybe a program like Win Patrol could help to see what programs on your PC are doing and stop certain actions before they're executed.
Another idea might be to install a VMWare instance with Ubuntu or Linux Mint or whatever, then use a Unix FTP program. Nothing on your computer is going to be smart enough to see into your virtual OS and hack your unix!
Maybe try LFTP
http://lftp.yar.ru/