Am I reading the situation correctly? Is there any way I encourage the other end of the link to throttle back?
Good FTP software, like the kind that is stock in Tru64, does rate-limiting. But not all ftp software does. If you've got a Linode (or equivalent) you could transfer to there, then transfer home, with control over the remote end. Also if your ISP has a cache, you could use it for rate smoothing, as the negotiation cycle will go quicker against a nearer remote endpoint.