Is that perhaps because you don't have a good understanding of the history, or is it perhaps because recent changes affect you more strongly than old ones?
If you were a Catholic 500 years ago, wouldn't you have complained bitterly about the upheavals in the 1500 year old Church caused by Luther and those inspired by him?
If you were a Catholic in England, when Henry VIII broke from the Catholic Church, wouldn't you again be complaining about the discontinuity?
I don't see why the large-scale changes of the Reformation are less discontinuous, for someone living in that period.
You wrote: "one of the things that fascinates me endlessly about the christian traditions of my community, is how many aspects of it are obviously echoes of pagan times."
This was part of a deliberate plan by the Catholic Church to co-opt local religions. It wasn't really "organic."
I know the history better in the context of the Spanish colonization of the Americas. The Catholics would come in, tear down the old places of worship, and build a cathedral on the same site. They would identify important stories, rituals, dances, etc. associated with the old gods, and recast them to the saints. This practice is known as Interpretatio Christiana.
This synecretic approach helped spread the religion, by making it a more tolerable replacement for what was before.
You write: "in antiquity, becoming literate and trained in classical philosophy was very much a "1 percenter" thing." You may want to read https://en.wikipedia.org/wiki/Literacy#Ancient_and_post-clas... and the given references like https://www.academia.edu/13211795/_Ancient_Literacy_in_New_T.... It seems that the during the 1990s and early 2000, it was though that about 10% of Rome was literate, and that more recent research suggests it was rather higher at perhaps 30-40% .. until the fall of the Western Roman Empire. That period of heightened literacy corresponds to the early Church, so it reflects the general culture and not something special about Christianity.
You write "Turning a church into a hipster lounge is so much more drastic than turning a pagan shrine into a church, or a church into a mosque."
Wow. Really? "Hipster" is a derogatory term meaning "I'm getting old and don't understand kids these days, so I'm going to call them names to make myself feel better."
I'll give an example from the Interpretatio Christiana Wikipedia page: "when Benedict took possession of the site at Monte Cassino, he began by smashing the sculpture of Apollo and the altar that crowned the height"
Would you rather have the sculpture of Apollo shown as artwork in a hipster lounge, that anyone can see, or destroyed to make way for a Catholic church?
The French revolution is hardly "current". The modern France - a mostly secular country - has a lot of archeologists and archivists trying to identify and preserve history, including non-Christian history.
Regarding your sarcastic quip, please stop trying to force things into a dichotomous world. We have only to look at the misogyny and racism of many of the "stars" of atheism to see that a lack of faith in a god has very little to do with good ethics.