Joko raised some great points during the final confrontation. Specifically, how everything happening now is our fault. Whether through ignorance or through a sense of vengeance driven hubris, Kralk being awake and even more powerful is a direct result of our actions. The near extinction of the Human race would not have happened had we not been so arrogant after meeting Joko in the mists.
Without getting into possible spoiler territory, can Anet say whether or not the Commander will face any ramifications for our actions from Tyria at large?