I would argue that he knew he "had to" keep the airbenders subdued and hidden away. Zaheer's combat advantage was basically that he was an airbender, and most benders/fighters that would come up against him have very little experience dealing with an airbender. Up against an airbending master like Tenzin, his airbending fell well short. Also, airbenders are incredibly mobile, being able to fly great distances and do this quickly. Zaheer needed to capture Korra, and needed time for the poison to do it's work in order for them to murder her while she was in the Avatar state. This would be easily foiled by a group of airbenders who could fly off rapidly to get reinforcements, and fly around scouting for where they were hiding with Korra.
In the end, not only does Jinora, a soon-to-be master airbender, use her powers to find where Korra is, she also used her knowledge of obscure airbender techniques to subdue Zaheer. So it's pretty clear why Zaheer wanted the airbenders out of the action when you see who played such a pivotal role in defeating him.