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?

Another theory:

Mr Eko has not has any flashbacks concerning why he was on Flight 815. Is it possible that "Mr Oz" was frightened because they know Mr Eko? Remember, Eko had a habit of introducing himself as, "I am Mister Eko," and then, in the case of the drug smugglers, he pulled out that knife and killed them (afterthey commented that his reputation was true, the 'he truly had no soul').

Perhaps "Oz" thought that after confessing and telling him the he was now on the right path, the good path, that meant Eko had changed sides and was going to help the passengers by getting rid of him. I might also mention that the CIA has a reputation of using the drug trade in South America to further their own operations. Perhaps they tapped Mr Eko once or twice and he met up with "Zeke."

Does this sound possible?

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charlie98210
"Whoa!" she said. "Cry 'Havoc!' And let loose the dogs of war!"
And, like Banquo's ghost, they just won't go away.