Actually, it was mostly clergy who spoke out against the treatment of meso- and southamerican natives by the encomienda system. One of the main figures there was Bartolomé de las Casas.
Also, I am really astonished what is considered to be science, here. A guy knocking flints against one another until he figures out how to make fire is apparently already a scientist, even though he has no sophisticated notion of hypothesis formation, logic, theories, universal laws of nature, statistics, peer-review, ordering knowledge into a systematic body, hindsight bias, scientific controls, distinction of main- and auxiliary hyposthesis etc. pp. nor were they really interested in scientific explanations.
And it's not so different for mechanics nowaday. I talked to a car mechanic just today and he assured me that he isn't really interested in attaining universalized knowledge that fits into a system of knowledge when fixing a car, but in fixing a car. Yes, he will use the insights of science and materials and tools that we wouldn't have without science, but that makes him as little of a scientist as using an i-pod makes me - or anyone else - a quantum physicist.
Similarly, people in antiquity had central heating, the creatans had warm and cold water pipes in their towns and heated their houses through them in the winter geothermally. Egyptians made tooth implants from hippo teeth around a thousand years before christ, long before anything resembling the idea of science emerged within greek philosophy. We know from the old papyri that their explanations weren't scientific either, nor were they even naturalistic in character.
While there's little mystery to making fire for us, for him it prolly was quite a magical process, too. Even until today smith in indigenous people that developed metal working have a magical, priestly quality as masters of fire and formers of metals. Their explanations why something works are really, really unscientific, but nonetheless they are quite successful in their craft and as well in propagating it.
Science is not simply trying things until something works, but it has to do with dscovering universal laws, build theories and complexes of theories that form scientific disciplines. Saying that it is a simple trial and error process of a 'hypothesis-test-loop' tuntil there's success is oversimplifying what science is and consist in to a degree that hurts and is denigrating of the people who do the hard and intellectually challanging work of an actual scientist.
Lastly, @ Silas, you vastly overstate how bad the conditions were for people back then and how much the supposed increase in living conditions are due to science. First, that is quite dependent on the exact time and region you speak about - and it is the same today, for example the Arabian Emirates have a much higher - much higher - living standard of it's citizens than, say, the US, even though they are ruled by Emirs that declared Islam to be the state religion, free spread of religion is quite restrictet and you can call the country a muslim country by all rights.
Also, as I pointed out things like tooth implants, seperated warm- and coldwater pipes, use of geothermal energy, and many others were known quite early in the history of humankind, when the prevailing system of thought was a mythic one and how it was possible to have all these things was explained by mythical stories, which also were used to preserve said knowledge.
And even the prejudice of the 'dark' medieval age is mainly just that: a prejudice. Historically speaking, it wasn't that 'brutal time of rampant disease, no medicine, starvation, extreme levels of violence as a % of population, short life spans with brutal endings, superstitious and violent tribes, and fear and ignorance of the world around us' you want to make it for the greater glory of modern science.
Universities are a child of the middle ages, for example. In particular of the church. 12th and 13th centuries saw growth in economy and technological innovation - mainly outside of academic/scientific system but within traditional guilds that had a more hands-on approach then the theory-centered science of that and the the modern era (they were more interested in 'how to' or procedural knowledge than the 'know that/why' or propositional knowledge that science is centered around (though
modern science is technology oriented in that is orienting propositional knowledge towards application)). Arts and culture flourished in the romanesque and gothic architecture and art. Serfdom actually declined in western Europe.
The picture of the medieval age as a "time of ignorance and superstition" that placed "the word of religious authorities over personal experience and rational activity" is, historically speaking, a caricature manufactured during the renaissance and enlightenment and the latter ones did characterise the medieval age exactly like that because they held science and reason to be superior to religion and faith (Davies Europe pp. 291–293 and Lindberg "Medieval Church Encounters" When Science & Christianity Meet p.
, when this actually is a distinction that wasn't alife in the medieval age, where science, reason, religion and faith merged in the scholastic worldview. And no, peole didn't either die at the age of 40, usually. Either they died young or much later at approximately the same age as later on up to the 18th century - where it went down with the industrial revolution only to recover later again. (even in the upper paleolithic life expectency was closer to 54 years if one survived the comparatively vulnerable state of childhood.) So, what later application of science really did was reducing child mortality quite a bit, which is really great, but it's not like everyone died at 40 years back then -
that was the work of applying science in early modern times.
These myths about 'them olden times before science helped us out' are shown to be such - maybe ironically - by modern historical and archelogical science.