One of the reasons prayer and religion integrate so poorly into otherwise secular media is that God doesn't make very good set dressing. You can try to neuter religious practice by sentimentalizing it (formerly the most common approach -- the young child offering innocent prayers), or by limiting its presence to moments of high drama and human bafflement (also common -- the protagonist crying out to God), or by demonizing it (now most common -- the psychotic zealot, the clerical predator), but seriousness about things divine logically demands a reorientation of interest away from the mundane concerns of the typical secular narrative and toward God. (When there is eternity to be gained or lost, the passions of the flesh and the pursuit of worldly peace seem rather thin.)
This demand for reorientation is jarring to the secular storyteller on two levels: (1) it threatens the integrity of the plot and the intelligibility of secular character arcs; (2) it forces the narrative into a conversion pattern, which cannot (by the lights of the secular writer) be done in a gratifying way without yielding to moralistic cliches.
One of the normal features of realist narrative is the absence of a clean resolution to the driving conflict in the plot. In secular realism, this lack of resolution is undergirded by a tacit nihilism or absurdism: there is no happy ending because life itself is an unresolvable series of tensions. But this lack of resolution seems to belong more properly to religious narratives, because the "locus refrigerii, lucis et pacis" which provides satisfaction for our struggles is not visible in this vale of tears, to which all our stories must be confined. Like the life of St. Francis, the best religious stories end in a place of suffering and decay, with an ellipsis pointing to eternal life.