No, I would not characterize Michael Obi as a villain.  A villain would typically be considered inherently bad.  He is, however, not very thoughtful or considerate when it comes to the traditions and legends of the villagers.  Despite being told about the path that was sacred to them, he still has the fence put up so they cannot cross it.  This was extremely disrespectful and a great insult to the villagers.  He should have thought more carefully about this decision. Had he let the path be, it would not have affected the school.  He wanted to be in control and he overstepped his boundaries.  As a result, he is retaliated against and some of the school is destroyed.  

Is Michael Obi a villain or a hero in "Dead Men's Path"?

While Michael Obi is not really a hero or a villain, he comes closest to being a villain. He hopes to be a hero, bringing modern ideas to the villagers; he acts, however, with "misguided zeal," and to the villagers, he would likely be seen as a villain. 

Michael Obi, who has just been named headmaster of the Ndume School, sees the school as "backward in every sense of the word." He is young, energetic, and modern and hopes to bring a positive change to the village. Yet his inability to respect the villagers and their customs and beliefs shows arrogance and makes him appear as more of a villain to the community.

Despite the fact that the footpath has sacred importance to the villagers, Obi insists on blocking the pathway with sticks and barbed wire. When a villager explains that the path is used by the dead to depart and visit the living and by children being born, Obi responds, "The whole purpose of our school [...] is to eradicate just such beliefs."

While Obi believes that he is acting admirably by teaching the children to laugh at the ideas of their ancestors, he is being insensitive to the culture and heritage of the community he has entered by trampling upon their customs, just as the villagers trample upon the schoolyard.