The reason would is being used in place of did is to avoid asserting the premise of the statement. That is to say, did states that what you're questioning actually occurred and you're questioning why, where would merely questions why.
By shifting the tense of the word to the future, you do not acknowledge the thing in question definitely happened. Instead, you are asking hypothetically why the thing would ever occur - you are asking about the possibility of occurrence. For example, the meaning of these sentences is fundamentally different:
Why would you jump off the roof?
Why did you jump off the roof?
In the second case, you did jump off the roof, and you're being asked why. In the first case, you might have, but you might not have; the sentence would work in either case.
The reason for the difference is this passage is dealing with religion. Although the book seems to be supporting religion, the sentence was likely written this way to avoid sounding ham-handed.