This is getting a bit armchairy, but here's a few points about it:
1- A civilization doesn't need piety in order to achieve technological superiority, Piety sometimes and most times goes against advancing. Of interest is the impecable achievements in the Muslim Empire, that for the most part had more to do with secularism and wealth than religion itself (though religion helped getting that wealth).
2- As mentioned before, it is a mix of secularism and wealth that usually provides a solid ground for science. Some of the early European Christian scientist had the hardest of times either coming up with new theories (because it would go against their beliefs) or getting them published to begin with (would go against the beliefs of the ruling classes). The Scientific revolution took generations to get anywhere, from kepler's shy attempts to revive interest on the Copernican system (even though it made far more sense than the Ptolomaic and Tychonic systems) to Galileos rather embarrasing trial (which was far less dramatic, yet still a shameful sign of the times).
3- The Scientific revolution really began when rationalism was fully on it's way, now the game over simplifiest this, but for the most part the most prominent scientists of our time have nothing to thank religion for. Newton, for example, was a pious christian, yet he spent countless of hours trying to decypher secret codes in the bible, occultism and alchemy (another topic of mysticism just not mixing with science). His real advancements are vastly smaller than his non-contributions in the occult.
4-When the first optical instruments were made, early "scientists" spent countless hours making absurd and ultimately useless contributions on worshiping the fine details of the "work of god" through these instruments. Sadly enough if we made a book about discoveries and real scientifical discoveries, let's just say that the first 5 pages would cover the rather anecdotical and cute discoveries made before the 20th century (useless sciences, the basics of chemistry and physics, steam power, electricity and calculus being it's main highlights). Real Science began around the turn of the century, when tools were perfected, when perceptions changed and secularism was in full swing.
If the last statement sounds bogus, it's likely because our education can be rather simplistic about these things in School. eg: do you know the states of matter?, liquid, solid and gas?, does anyone really thinks scientists still work with that obsolete ass theory?
http://en.wikipedia.org/wiki/States_of_matter
Science is supposed and meant to always be advancing, you can have early knowledge of psychology as a reference, but no Psychiatrist or Psychologist still uses Freud or Jung. Same thing as a biologist having Darwin as an early early reference, but not using The Origin of Species as the basis of his work. Science is meant to be constantly changing, religion however doesnt have that quality (it actually does... when it's secular).
The game, and trying to get back on topic, could be a bit more forgiving perhaps. It would be hard for an early scientist (likely a higher member of society) to have been agnostic at the time and there probably should be an option to be pious and rational at the same time. America for example would be a civilization that is Pious and Rational at the same time, yet Civ 5 doesn't allow that.