Actually what causes anaerobic bacterial activity is low or lack of oxygen/gaseous exchange (anaerobic means without air). If you make a drainage layer like you're proposing, this would not create anaerobic conditions. With the drainage system Kurt describes in his care articles (and I've seen in person - I will photograph it next time - Kurt doesn't have a camera), he sticks a siphon hose down the big tube he uses to access the water layer. You do need to siphon it when the water builds up down there.