Is the stop_on_ratio setting working for you?
In my /opt/etc/rtorrent.conf i have the line stop_on_ratio = 120 but this morning i recognized that there was a torrent with a ratio over 2,2 and still seeding?
So it seems that this command was not recognized by the client.
Edit:
The stop_on_ration command like it is showed all pver the Thread is simply wrong. It has to be combined with a scheduler Task, like it is explained in the sample rtorrent.conf.