Well, religion used to be science/knowledge in the past and those terms got separated when monotheistic non-gentile religions took over. Religion was seen as a national identity story in the process and later on it was just devoured by the new Churches.
If by non-gentile you mean Abrahamic religions, then that's pretty wrong: Religion, Philosophy and Science were actually merged into one by those, they did not split them. Through the Middle Ages the Churches were the ones protecting science and philosophy from dying out, while the Muslim world was a bastion of science and philosphy. Abrahamics did not even consider you a religion if you did not put enough importance into Philosophy and Science (and in return philosophies like Confucianism were seen as religions by them due to high focus on philosophy and science). It wasn't until after the Protestant Reformation that those concepts started to be viewed as separate once again (possibly influenced by the Protestant Literal Interpretation of bible leading to numerous conflicts with scientists, as well as many scientists not wanting to be too closely affiliated with these warring churches).
Remember that if it's Rome II, Rome will probably not be the sole country playable. We will probably have other civilization available where religion was predominant (the first that come to my mind is Egypt).
Still won't matter because at most it will be a few buttons and bonuses, like in first Rome. You won't see big religious conflicts (like ones between Catholics and Muslims), nor religious conquests with intent to just spread the religion (like the First Caliphate), nor civil strifes caused by religions (like Protestant Reformation and Christianization of Rome). When it just affects one nation and it's always the same religion, than religion as a gameplay feature is minor. More precisely, it is more of a cultural feature than a religious one.