"For confession to mean something you must have a penitent heart" = Eko's brother the Priest
I am taking this and the black smoke to mean that Eko has confessed his sins and now has a penitent heart. Not speaking for 40 days after killing 2 Others has to have some kind of penitence to it as well.
Eko is not a "bad guy" anymore. I think that he always thought of himself as a good person, i.e. not shooting the boy after slicing the two guys, but that he would be dead and possibly his brother if he didn't continue as a warlord type guy. I think when his brother was shot he really changed to a good person.That is why he answered yes to the question of whether or not he was a priest.After he killed the 2 others, he did stop talking for 40 days because he considered himself a priest and even though he did it in self-defense he did it as you said to serve his penitence.
Eko is the yang to Locke's yin. Locke is the Good half (yin), which contains a touch of Evil within it; Eko is the Evil half (yang), which contains a bit of Good.And if my earlier theory pans out (about Locke representing Gilgamesh, and Eko representing his enemy/friend Enkidu), then Eko, alas, will eventually be killed...but not before he and Locke together defeat (or at least face) a common enemy. This has already begun to happen, with the two of them facing down the smoke monster.