Projects are always done the same way, via compartmentalization. You can work on one aspect of a greater project without actually being privy the the details and execution of the project as a whole. Look at how planes are built. Large teams of people who never have contact with eachother as they are assigned very specific tasks that they focus on.

I don't deny they Christians have been targeted all over the world in a similar fashion. A lot of people in Gaza and Lebanon are Christian, for example. They definitely bombed those cities, but they never nuked them. I recommend skipping the dissonance and preconceived beliefs and reading that book.