One could reasonably argue that the central conflict playing out in The Children of Men is not so much between religion and science as between a religious view of life and one that is influenced by a warped understanding of science.
In the dystopian society depicted in the story, science is distorted by the state in order to help murder the elderly, who are deemed to be a burden to society. The abuse of science can also be seen in the state-sponsored program of compulsory sperm-testing and gynecological examinations conducted on healthy men and women in order to find fertile individuals.
This program involves treating people as means to an end rather than as ends in themselves. In treating people this way, the state is demonstrating clearly that it has no conception of individual worth and autonomy. People exist for the benefit of the state and for no other reason.
In contrast to this scientific, life-denying attitude, we have the life-affirming values of the Christian faith as exemplified in the actions of The Five Fishes, a dissident group dedicated to overthrowing the dictatorship of Xan Lyppiatt. When Xan's cousin Theo Faron shoots him dead at the end of the story, the forces of Christianity have gained a huge victory over the science-centered creed that formed the basis of Xan's dictatorship.
However, that victory is by no means total. Theo's putting on of Xan's Coronation Ring suggests that the system over which his late cousin presided will continue for the foreseeable future, albeit in a much more benign form. Nonetheless, Theo's making a cross on the forehead of Julian's baby does appear to hint at the distinct possibility that Christianity will play an important part in English public life from now on.