This episode we get to focus on Eko, learning more about the guilt that seems to drive him. After Eko took over the priesthood from Yemi, he tried to stand up to those abusing the members of the church. Unfortunately, because he slayed the men inside, the people of the village destroyed the church, saying Eko had defiled a sacred place. He builds a church on the island because he must pay for the one his actions destroyed.
He also seems to owe God for the lives he has taken, but this is a struggle for him because every life he has taken was to protect someone else. Now he faces the blood on his hands, wondering if the results of his actions do indeed justify his sins, or if there really is no justification for such a deed. He has only done what he's needed to survive, depriving those of life who are committing evil actions so that he can continue protecting those who need his help. Yemi (or some ghost/projection of him) still calls Eko to confess however. But Eko sees nothing to confess. He is proud of his actions and believes he has made the best of the life he was given. But this Yemi has no compassion on Eko, which leads me to believe that this is not his brother but the island confronting Eko. And in the island's view, Eko can do nothing to justify his acts. The smoke monster attacks and kills him. Judgment has come. And if we are to believe Eko's last words to Locke, the rest of them will face it soon.
Though the island saw Eko's decisions as beyond forgiveness, how would each of us respond in a similar situation? Eko's life was not an easy one, and he continually sought what he could discern was best. Each of us does the same with each decision we come to, and this episode helps us remember to not make our choices lightly. But thankfully, God is more merciful and forgiving than the island, and ultimately has the final judgement on Eko's soul.