It's true that the DM will only be rewarded once for running a particular adventure in PFS. However, this results in the DM/group purchasing more adventures to run which benefits the publisher. In turn, the DM gains access to a wider pool of rewards to draw from for his/her character, including magic items. If I was part of Paizo I would simply respond to your observation by referencing General Mill's Total cereal ads that used to say something like "It takes (x) bowls of your cereal to match the nutrition in one bowl of Total." Point being, the rewards are substantially greater in PFS than AL. You would need to run an AL adventure several times to equal the gold and XP rewards compared to a PFS adventure, let alone the value of the magic items or other adventure rewards (PFS liberal attitude regarding magic items is a whole separate issue).
It's good to hear that DM rewards for AL are being increased. Coaxing more people to sit behind the DM screen is a good thing that enables more players to participate.