Yes, absolutely. Science and religion are opposed, and you shouldn't expect a discussion of one to defer to the other.
There is no justification for a science program to be intentionally biased against religion or to mischaracterize religion in order to fit a false narrative. Science should not have an agenda and should be free to follow evidence wherever it leads. This Cosmos series is a mixture of Hollywood and science – and Hollywood comes with its own agenda , beliefs, and ‘faith’.
Beyond this, the ‘conflict’ between science and theism is fairly new. Excerpt from Pulitzer Prize-winning author Daniel Walker Howe’s What Hath God Wrought: The Transformation of America, 1815-1844, p. 464:
As this chapter is written in the early twenty-first century, the hypothesis that the universe reflect intelligent design has provoked a bitter debate in the United States. How very different was the intellectual world of the early nineteenth century! Then, virtually everyone believed in intelligent design. Faith in the rational design of the universe underlay the world-view of the Enlightenment, shared by Isaac Newton, John Locke, and the American Founding Fathers. Even the outspoke critics of Christianity embraced not atheism but deism, that is, belief in an impersonal, remote deity who had created the universe and designed it so perfectly that it ran along of its own accord, following natural laws without need for further divine intervention. The common used expression “the book of nature” referred to the universal practice of viewing nature as a revelation of God’s power and wisdom. Christians were fond of saying that they accepted two divine revelations: the Bible and the book of nature. For desists like Thomas Paine, the book of nature alone sufficed, rendering what he called the “fables” of the Bible superfluous. The desire to demonstrate the glory of God, whether deist or – more commonly – Christian, constituted one of the principal motivations for scientific activity in the early republic, along with national pride, the hope for useful applications, and, of course, the joy of science itself.
What's all this extra baggage that I never said? It wouldn't be correct for anyone to mischaracterize anything or make it fit a false narrative. But I never suggested that did I?
Science by definition is biased against religion. Religion doesn't require evidence and makes a virtue of believing in things without it. One of the fundamental ideas of science is to reject that idea. Of course it's biased against religion. If one chooses to take the religious approach seriously, fine. But it's not reasonable to expect that science should do so.