SSS: Christianity and Islam have played a huge role in the shaping and destruction of African cultures. The fact that missionaries were a necessary part of successful colonization was not lost on those rebelling against colonialism and imperialism.
Religious missionaries have always been used as a front line colonial assimilation tool. And especially since the advent of the printed word which makes the spread of political ideoology under the guise of "religious insruction" particulary powerful.
And let's not forget Heinrich Himmler, the leader of the Nazi SS, whose post-war plans included using the Jehovah's Witnesses as a way to keep Germany's conquered lands under control. He was especially impressed with their ideology of loyalty and non-poltical stance.
SSS: From the very early uprisings in Africa (particularly the Mau Mau uprising) missionaries were particularly targeted for being associated with colonialism and I can't say I blame them.
The WTS has had a presence in Africa almost since the very beginning of the Bible Student movement. I don't have all the dates and such...this is from my "cole's notes/memory"...but from what I can recollect, the WTS lost control of the Bible Students in Africa quite early in the 20th C. It was only later...not sure the year, after much political turmoil involving the political influence that the JWs/WT movement had in African politics, that the New York WT Society got control of the JWs in Africa again after making deals with African governments.
...or something like that.
The Jehovah's Witnesses/WT movement in Africa is still fairly fractured, with offshoots emerging and/or still hanging on to the WTS control.