Really interesting post @clausewitz! This is one of the topics I focus in my work, but from the philosophical point of view! So much to say, but I'll just tell you for the moment that you're not alone in thinking this!! Brut positivists and empiricists always get trashed in the humanities :)

Have you read Horkheimer and Adorno? (their original texts, in German, are meant to be amazing) Horkheimer's the philosopher who started and coined critical theory in the 1930s, here's a link to his amazing piece in which he defines the term for the first time:
https://sisphd.wikispaces.com/file/view/hork1.pdf
He starts from a critique of scientific modes of thought and models before offering critical theory as response. Critical theory was initially meant to be an interdisciplinary endeavour bringing social theory and empirical research, and scientific research together (this is what he did with his team at the Frankfurt School).

Another author you might find interesting is Bruno Latour. He's a sociologist/anthropologist who spent a lot of time studying scientists in labs and really picks apart the social activity involved in creating scientific models and knowledge. I don't know if scientist talk much about the Science Wars of the 80s-90s? It was a huge thing amongst philosophers of science. Latour was one of the main protagonists coming from the humanities, along with Isabelle Stengers (she worked with Illya Prigogine, a chemist, who was also a big player in this debate).

Far from saying you're wrong, you should find comfort in these readings as they explore the social construction of facts, both in the lab and in society. The first time I read both authors my mind f-ing exploded because their work encompasses so much more than just critiques and analyses of science, even if that's their starting point (partly).

I am actually writing a post on epistemology at the moment which will touch on some of the points you mention, I'm using some of the authors i mention above plus other favourites :)

Thanks for sharing your interesting thoughts! Hit me up if you want to talk more about any of this :)