If you only heard about the ABA lawsuit in the Chronicle's news section you might believe the spin that independent bookstores are doomed. Heard that before. So far, it's a draw. Illegal, unfair practices were documented at the trial. Due to this and previous lawsuits, publishers have shaped up.
Secret deals are less frequent.
A special deal for one company more often now is offered to all bookstores. The fate of independent bookstores and chains alike is in the hands of people who read books and buy books. Where you shop is a political, personal decision.