Even though Nexus 9s are supposedly "built to obey", they can still get "off the rails" after a traumatic experience. Hence why there is a Baseline Test as a fail-safe mechanism to ensure Nexus 9s act like Nexus 9s, and don't start having "human" emotions. It's a mean for brainwashing.
We are not quite sure what happens after a Nexus 9 fails the test. I assume they either get retired, or they get a special training that emotionally boosts them back to baseline (in other words, they get brainwashed again). The reason why Officer K was let off the hook is that he claims to have killed the child. Remember, at this point, he thinks he is the child, which leads him to believe he is not a Nexus 9, but a brainwashed servant.
So not only is he actively in the mood for rebellion after such an infuriating realization (that he had been brainwashed all along), he also has to protect the truth that he is the child, in order to survive.