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.