The advantage of anti-religious polemicists over those who find themselves firmly entrenched in politics or religion may be an advantage of perspective. If we think of the three realms in terms of their relation to time, the religious realm has a tendency to be married to the past (especially the Jewish and Christian traditions which are tied to historical events), the political realm is primarily concerned with the present and the crises of the moment, while the scientific realm has the future as its target. In this way, anti-religion polemicists can pit religious past against the scientific future. They lay claim to all the positive discoveries of the past and all those as yet undiscovered. For instance, the scientific realm can lay claim to both contemporary treatments for cancer and finding the cure for cancer without, of course, taking responsibility for the development of chemicals, devices, and circumstances which increase the risk of cancer.
Yet, when the history of the world is told in a way that pits science against religion, the scientific realm has the advantage of having no living history, no tradition. That is, the anti-religion polemicist can divorce himself from the errors and atrocities of the past in a way that neither the politicians or the religious can. The scientist can forget the practice of bleeding as a cure for fever in a way that the Church cannot divorce herself from the Spanish Inquisition. Since science is concerned with a certain type of knowledge and technological development, all mistakes of the past can be presented as "We now know..." or "If only, they had known..."
What if we wrote a history of science that focussed only on the "bad" science? Would science fair so well? If we focussed our attention on such things as bleeding, Thalidomide (or other modern birth related experiments), the disparaging and persecution of midwives, DDT, the atomic bomb, machine guns, biological and chemical weapons, racial profiling etc or focussed only on evils done in the name of science like vivisection or profiled only figures like Joseph Mengele, then would science lose some of its shiny veneer. Yet, scientific history has a way of dissociating itself from its errors (experiments) and faulty assumptions because in many ways the ends justify the means. The discovery of insulin by Banting and Best through experimentation on dogs would be one sided if we only focussed on the rights of the animals without due attention to the incalculable benefits to diabetics.
Many people tend to accept that evils done in the name of science were "bad" science and so don't really belong to the history of science. Yet, when Christians claim that evils done in the name of Christ are "bad" religion, the same acceptance is not so forthcoming. For Joseph Mengele was not doing science, he was doing Nazi politics and, of course, we all are supposed to know that Hitler was a Christian and his religion was the source of his anti-semitism. The advantage of the scientific realm with its future orientation is that the future remains pure. The future is not muddied by politics and religion. That is, the future is not muddied by reality. Scientific errors of the past can be shifted onto the backs of politicians and priests and science herself can remain pure and free from sin.
The truth is while these realms exist they have never been and can never be separated. There is no pure science that stands outside religion and politics. Science cannot be performed in a vacuum. Christianity has always taught that sin poisons everything. So, that the Church and State are corruptible does not come as a surprise to most Christians nor is the reality that scientific knowledge can be used for good or evil.
For those who are interested in reading about the relation of religion and science and the rise of the religion versus science myth, I would recommend either the short chapter in Christianity on Trial: Arguments Against Anti-Religious Bigotry
by Vincent Carroll or for a more in depth academic treatment of this subject with lots of footnotes see Rodney Stark's For the Glory of God: How Monotheism Led to Reformations, Science, Witch-Hunts, and the End of Slavery
. Stark also tackles the questions of Christianity's relation to the Inquisition, Witch-hunts and Slavery. Carroll grapples with many of the popular arguments against Christianity including the Inquistion, Nazism, and the environment.