The potential for division between science and religion can be seen in a couple of places here. The first would be the Jesuit priest's crisis of faith might be, in its own right, an example of the division between science and faith. He leads an expedition to this new planet and believes in space exploration. At the same time, there is an unending source of pain in his own heart about the nature of religion and God. Whenever a priest holds moments of conflict in their own heart, a challenge to religion is present. At the same time, there is some strong level of questioning as to why God would destroy this community. From all data, it appears to be similar to Earth in being humane, compassionate, and understanding. If they were able to consider how they would be viewed after the supernova, it seems to be an advanced culture. The question results here would be that if God was benevolent and powerful, why would he allow this culture to be wiped out? Why not save them? The ending, of course, with the culture's destruction coinciding with the birth of Christianity helps to evoke the challenging nature of any singularly driven mode of spirituality. The fact that science is what brings this out might be another source of conflict between it and religion.
The conflict here comes about because the speaker in the story is having a hard time reconciling what science has told him with what his religious beliefs tell him.
He has just found the Star of Bethlehem -- the one that the Bible says showed where Jesus was born. But when he finds it, he finds that a perfectly good civilization died in order for that "star" to be visible on Earth.
He is unable to understand how God would allow an entire race of beings to die so that this new religion could come about on Earth.
To me, his dilemma doesn't make sense because Christianity does not say that God caused the Star of Bethlehem in order to mark Jesus' birth. So I don't see why he can't just think that God used this thing that was already going to happen as a sign for Jesus' birth. But what I think isn't important here...