Do Changes in the Understanding of Religion Mean a Defeat of Religion?

According to Eliezer Yudkowsky, the changes in the way religion is understood are a retreat:

Back in the old days, people actually believed their religions instead of just believing in them.  The biblical archaeologists who went in search of Noah's Ark did not think they were wasting their time; they anticipated they might become famous.  Only after failing to find confirming evidence - and finding disconfirming evidence in its place - did religionists execute what William Bartley called the retreat to commitment, "I believe because I believe."

Back in the old days, there was no concept of religion being a separate magisterium.  The Old Testament is a stream-of-consciousness culture dump: history, law, moral parables, and yes, models of how the universe works.  In not one single passage of the Old Testament will you find anyone talking about a transcendent wonder at the complexity of the universe.  But you will find plenty of scientific claims, like the universe being created in six days (which is a metaphor for the Big Bang), or rabbits chewing their cud and grasshoppers having four legs.  (Which is a metaphor for...)

Back in the old days, saying the local religion "could not be proven" would have gotten you burned at the stake.  One of the core beliefs of Orthodox Judaism is that God appeared at Mount Sinai and said in a thundering voice, "Yeah, it's all true."  From a Bayesian perspective that's some darned unambiguous evidence of a superhumanly powerful entity.  (Albeit it doesn't prove that the entity is God per se, or that the entity is benevolent - it could be alien teenagers.)  The vast majority of religions in human history - excepting only those invented extremely recently - tell stories of events that would constitute completely unmistakable evidence if they'd actually happened.  The orthogonality of religion and factual questions is a recent and strictly Western concept.  The people who wrote the original scriptures didn't even know the difference.

In related news, I've recently been trying to think of how to explain non-Euclidean geometry (or, what's worse, Cantorian set theory) to ancient Greek mathematicians. Is today's mathematics the same as their mathematics? After all, ancient Greek geometry made falsifiable claims about Earth measurements.

When considering whether change means the original idea is gone, I'm reminded of the following story about Fermi:

Enrico Fermi once attended Robert Oppenheimer's students' seminar - and couldn't understand a word of it. He was cheered by the last sentence however: "...and this is Fermi's theory of beta decay."

and a similar story about Galois Theory:

When Emil Artin taught Galois Theory, he did apparently discuss Galois's own approach. He tells an anecdote to the effect that he asked one of his classes how much of his book on the subject Galois himself would have recognized, and one of his students suggested that probably the title would have been the only recognizable thing in the whole book. And then another student said, "No, he probably would say, 'Okay, Galois, that's me, but who's this guy Theory?' "

By the way, grasshoppers do have four legs. They also have two other legs.