Capture rate on the PokeAdvisor is most definitely calculated by Caught/Encountered. And on my real account (never used bot) i got 97% capture rate (582 caught 600 encountered). So if they ban everyone over xx% some legit people will be fucked. Wasting pokeballs won't lower the statistic, but if running away will that would be the better option. If running away from the capture would lower the statistic, pokefarmer should add an option to choose wich pokemon to add to the "capture -but run away"-list.
Sorry for /rant and horrendous english