transmission-cli is perfect. I use rtorrent mostly for my actual torrent needs, and the rutorrent front-end. The main developer of rutorrent has made some great plugins for it, one of them uses createtorrent to make torrents. I think it must work fine on linux....i've informed him of the issue with it on FreeBSD and i'm pretty sure he'll add support for transmission-cli. The syntax is VERY similar so i doubt it's REALLY hard.
I've also emailed the developers of createtorrent to let them know how bad it is on FreeBSD....It shouldn't take an hour to make a signle torrent.
EDIT:
if anyone cares, the developer of the rutorrent webui for rtorrent has added transmissioncli as another options instead of createtorrent for the create plugin. thanks again for the suggestion to try this. Just thought i'd edit the post as a followup if anyone cared.