I just read thru this. You know that you actually prove my statment in a number of ways... right? In many ways, science is propelled by religion one way or another. In other words religion has been the driving force for scientists weather they were for the notion or against. The idea that Civ 5 makes you choose one or the other makes no sense to me at all. It's almost like the makers of Civ 5 believe that it is rational to have no belief in a mastermind maker? It has not been proven by science that there is no mastermind maker (God).
A social policy tree is a civilisation's focus - not whether it has it at all. You can still trade without the commerce tree, have traditions without the tradition tree and order without the order tree - it's whether your civ has made a specific commitment to prioritise one of those aspects of their society.
Piety as a social policy is not about whether you have a religion or not, but whether religion is a focal trait of your civilisation, woven deeply into every facet of the country's being. The Greeks and Romans had gods, for example, but they weren't what you would consider pious by any stretch. England is another example of a nation that has gone very much more rationalist than pious, even though the Church of England is technically a state religion. Spain is very much a civ that would have taken the piety road, with the church having a strong influence in the running of the country for a long time.
The choice is not science vs having a god; but more whether religious vs secular institutions dominate your power structures, and whether you choose to preference understanding heavenly matters vs worldly matters.
The Wikipedia article for "Age of Enlightenment" summarises what I think "rationalism" represents pretty well, and why it is opposed to a focus on "piety", I think:
The Age of Enlightenment (or simply the Enlightenment) is the era in Western philosophy, intellectual, scientific and cultural life, centered upon the 18th century, in which reason was advocated as the primary source for legitimacy and authority. It is also known as the Age of Reason.[1] The enlightenment was a movement of science and reason
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The "Enlightenment" was not a single movement or school of thought, for these philosophies were often mutually contradictory or divergent. The Enlightenment was less a set of ideas than it was a set of values. At its core was a critical questioning of traditional institutions, customs, and morals, and a strong belief in rationality and science. Thus, there was still a considerable degree of similarity between competing philosophies.[3] Some historians also include the late 17th century as part of the Enlightenment.[4] Modernity, by contrast, is used to refer to the period after The Enlightenment; albeit generally emphasizing social conditions rather than specific philosophies.