This is a stretch, and more of a stream of thought, but maybe there might have be a third man that tried to take him away the night that he killed those two others?
They were trying to kidnap the "good" tallies? Eko made his apology/confession to Henry to show that he has changed his path to good?
When Eko looked into the Black Cloud, were they images of the bad things he's done or the good or both?