Sam's former SEAL life has left his heart scarred, especially after Moe's death. In "Lokhay," Sam was called on to help an Afghani elder, Yusef, find his missing nephew, Amir. Yusef was responsible for saving Sam's life, so there was nothing that Director Granger or Hetty could have done to prevent the agent from investigating the disappearance.
Sam has a strong sense of honor and obligation, plus a big heart. Those traits help him as an agent, but in this situation they put him at odds with his job initially.
Eric ignored the orders to leave the investigation alone, reviewed the traffic camera footage, and traced the abduction to a highly sought after terrorist known as The Ambassador, Haakim Habib. This evidence opened the doors for Hetty and Granger to assign an official case to Sam and the NCIS team.