why doesn't thresh kill katniss?

Thresh lets Katniss go because of what she'd done for Rue. He learns that Katniss was not only Rue's ally, but that she had killed the person who attacked Rue as well. It was a matter of restitution.

Thresh realizes what Katniss has done for Rue, and not only did he know that Katniss was Rue's ally, but he knew that he had killed the brutal boy who had killed Rue.