Knowing the high quality and thoroughness of the answers you usually give on enotes, you're probably after more than what I can muster for an answer to your question. But no one else has answered yet, so just in case you're in a hurry I'll venture a try.
Okonkwo kills Ikemefuna for precisely two reasons, though whether or not they are "good" is up to interpretation.
Ikemefuna's status in his new tribe is precarious from the beginning. It seems he is left with Okonkwo for three years almost out of neglect. No one seems to make a decision about him. The tribal elders leave him with Okonkwo almost out of default. One day, for no reason that is revealed, the elders decide to kill the boy. Okonkwo goes along with the elders as he always does.
During the killing itself, the boy runs to Okonkwo for help after receiving one blow from a machete, crying, "My father, they have killed me!" He uses the term "father," which is pointed out earlier in the novel as being unusual under the circumstances. Okonkwo raises his machete and delivers the final blow, killing the boy. In the narrator's words, Okonkwo was "afraid of being thought weak."
Okonkwo goes along with the tribal leaders and is afraid to be thought weak, and thus kills Ikemefuna. Like I said, I don't know that the reasons are good ones.
I'll offer up two possibilities, neither of which I feel are exhaustive or all-encompassing, but do both coincide with his tragic flaw:
(1) Okonkwo's belief in and reliance upon tradition. When the elders decide that Ikemefuna should be killed, Okonkwo does not second guess or challenge their decision, just as he did not challenge the decision to place Ikemefuna with his family three years before. Okonkwo sees his adherence to the wishes of the village elders as part of his responsibility to his culture and tradition. We can juxtapose this to the warning of the eldest member of the village who warns Okonkwo against participating. However, this is the perspective of one old man and of the collective wisdom of the elders.
(2) Okonkwo's fear of the judgment of others, particularly regarding his own masculinity. In part because of the old man's warning, Okonkwo feels compelled to show that he is strong and devoid of emotion by participating in Ikemefuna's murder. Although it is suggested that Okonkwo has mixed feelings about this, his internal need to not appear weak or overly emotional in front of the other men of the village wins the day.
The two reasons why Okonkwo would kill Ikemefuna even though Ikemefuna considers Okonkwo as a father is because
1) Okonkwo was raised up with his culture and religion surrounding him. So it is most likely that if his religion tells him that something must be done, then it has to be done.
2) This reason is probably the most logical reason why Okonkwo would kill Ikemefuna is that he does not want to appear weak towards the others. He does not want the villagers to view him as a man who suddenly becomes weak and affectionate towards the boy, thus resulting in him killing Ikemefuna.