This isn't inconsistent with the purpose of the films. Like the other Jedi, Obi-Wan is a flawed character through the first three films. He doesn't live up to the pacifist and altruistic ideals of the Jedi in many, many ways. Lucas stresses this with a number of cinematic parallels to Luke in Empire.

This is why the ending of III is in sharp contrast to the ending of VI: Obi-Wan goes to kill rather than confront and forgive Anakin as a true Jedi presumably would. Even Yoda makes this mistaken in attacking Palpatine -- although he seems the only character aware of why he failed after the fact.