Why would an Igbo who killed a christian have to flee from the clan?

Because Okonkwo had been in exile for so long, he did not realize the extent to which British rule had taken hold in Umuofiya. Viewing the British administration and their Christian churches and schools as a temporary phenomenon, he expects that he and his followers can drive them away. The majority of the people have either converted or accept the presence of the Christians and understand the close connection between religion and rulership. The Igbo men’s crime of burning the church is inexcusable in British eyes. The situation escalates, including the arrests and beatings.
By the time Okonkwo is released, he has chosen his path. Based on the intensity of the British and their followers’s retaliation for burning the church, he knows that killing the messenger will bring down the full wrath of the administration. The others in the clan, even if they did consider him justified, fear the immediate reprisals and anticipate the longer-term consequences. They cannot take the chances of even seeming to support him. He no longer has a place in his clan.