When we say that the villages of Mbanta and Umuofia "accepted" the presence of the missionaries, we should be clear that we mean the villages tolerated the English people without embracing or approving of their presence.
Mbanta's governing body decides to allow the missionaries to stay for a few reasons, some clearly stated and others that we have to infer. We never get to see exactly what debates were held in Umuofia when the missionaries arrive there (because Okonkwo is still in his seven years of exile at that time). We only know that the missionaries arrived there before coming to Mbanta and they quickly gained a foot-hold.
First, we should note the context of the initial arrival of the missionaries in the nine villages. Umuofia and Mbanta are fully aware of what happened in Abame. Abame was wiped out because they killed one Englishman. This fact certainly influences Mbanta's response, although the elders do not say this directly.
The village adopts the attitude that Okonkwo's uncle, Uchendu, has advocated at this point in the novel: Do not act aggressively until you understand what the response to your aggression will be.
In their first encounter with a missionary, the people of Mbanta felt that the white preacher "must be mad," and he seems to pose no immediate threat to the village and its way of life. Okonkwo, leaving the meeting, "shrugged his shoulders and went away to tap his afternoon palm-wine," which speaks to the levity with which the people initially treated the missionaries.
When the missionaries moved into the village and were given a plot of land in the evil forest, the "inhabitants of Mbanta expected them all to be dead within four days." The Christians do not die, but do begin to absorb some members from the clan. The first converts to leave the community of the village are seen as "a good riddance" because they are troublesome people anyway (like the woman who repeatedly bears twins).
In Umuofia, the people "believed that the strange faith and the white man's god would not last." And the losses in the community were negligible.
"Chielo, the priestess of Agbala, called the converts the excrement of the clan, and the new faith was a mad dog that had come to eat it up."
When Okoli kills a sacred python and dies soon after, the villagers feel that the events prove that "the gods were still able to fight their own battles. The clan saw no reason then for molesting the Christians." While these attitudes allow the Christians to gain a foot-hold in Mbanta, they also demonstrate two basic aspects of the village's response to the missionaries.
There was a sense of unreality, disbelief and incredulity regarding the missionaries. And the view that the missionaries were unimportant was strengthened by a sense that the Igbo's gods would take care of any real threat if the Christians were to challenge their religion.
At first, the missionaries seem to pose no immediate threat and only take the undesirable people from the community. And, importantly in terms of theme, the conceptual conflict between the Igbo and the Christians that underscores the more physical and practical conflict takes place on the level of religion. As long as the Igbo believe in their religion, they are confident that the Christians will be dealt with in due time by the gods. In other words, they are not afraid of Christianity because they have their own religion and put their faith in it completely.
One of the major reasons that the tribe was not threatened enough to expel the missionaries is that they were given land that no one else wanted in the forbidden forest and the only members of the tribe who were attracted to them were the outcasts from the tribe. And though the missionaries condemned some of the traditions of the Igbo, they do not openly fight against the tribe. Mr. Brown, the first missionary, has made a point of building relationships with the tribe and trying to come to understandings with the tribal elders. This has allowed them to co-exist peacefully for several years while Okonkwo is living in exile.
But once the so begin to gain confidence because of their newfound sense of peace and worth, problems begin to arise that Mr. Brown and his wisdom cannot solve. Okoli begins the bigger troubles when he kills the sacred python, angering the tribe and starting them on the road to conflict with the missionaries.
This answer is a little unclear, is there another reason why?