What makes this incident of Okonkwo killing someone so different in things fall apart?

This incident is not specified. Assuming you are talking about Ikemefuna's death, the difference in this death was that it was not in war, and it was of his own adopted son. Okonkwo killed Ikemefuna because the Oracle had decreed it must be done. However, for Okonkwo to deliver the blow himself was unnecessary. Okonkwo did this out of fear, not out of courage.