What about Christianity? Christianity was brought into the country by English missionaries as you would probably have guessed in around the 1800s the same time as the colonialism set in. I would guess that people had their ways of worship, they call that indigenous. This is just my view but I think Christianity was imposed on people since they were thought to have unorganized ways of worshiping their God. The idea of God was there, it just wasn't formal.
How separate is the Church and the state in Kenya? Church and state in Kenya are separate formally but unfortunately the Church has a lot of control of what the government does. For instance the proposed constitution sought to legalise abortion, of course under some conditions but the Church strongly stands against such an idea. Reasons? They are not that clear.
Kadhi courts have been operating in Kenya and have not affected any non-Muslims as far as I know. I am pretty sure nothing has changed with the the demographic figure of 6% of Muslim population in Kenya to make it such a contentious issue in a country where the majority of the people are Christians. There are obviously bigger fish to fry in the proposed constitution but this particular one seems to warrant political airtime that should be worth so much to the taxpayers so to speak. Where do we get the time?