Is it possible to rate-limit an scp/sftp/rsync/etc transfer from the command-line? ie, manual QoS on a single command?

scp has -l, and rsync has --bwlimit.

Yes, there's an application that works exactly like your 'magic-qos-tool', called "trickle".

EXAMPLES
     trickle -u 10 -d 20 ncftp

     Launch ncftp(1) limiting its upload capacity to 10 KB/s, and download ca-
     pacity at 20 KB/s.

Rsync makes this easy on you, it has an option to do this: --bwlimit=KBPS