Buying second hand props up the $60US/$90AUD new cost though. Without second hand (ie. Steam at the moment) the prices plummet very quickly, $5 for Just Cause 2 for example, do you think GameStop etc. would allow you to buy it new for that price?
No, it's the other way around. Buying second hand denies profit to the publisher, which reduces units sold, which increases the price they have to charge to make any money.