My interpretation of the end

I think we are lead to believe throughout the movie that the two sisters are meant to have this profound awakening from religion as "exposed" by Mr. Reed but IMO the latter has the bigger revelation. In a way, both Sister Paxton and Sister Barnes are aware that there are "plot holes" in their religion but it doesn't distract them from its purpose and benefit to humanity. Mr. Reed, on the other hand, came to the conclusion that religion is about control and has no basis in reality and wants Sister Paxton to "see the light" and come to this same conclusion. In the end Sister Paxton gives him the answer he wants to hear but he fails to realize that she knew it all along rendering his entire "game" futile in the sense that it doesn't teach Sister Paxton a lesson or change her outlook on life but rather confirms the purpose of religion in her eyes. She still has faith but knows that religion can be used as a tool to control people which is ironically what Mr. Reed tries to do with both sisters, essentially playing God. The reason why Mr. Reed has the biggest revelation in the end is that right before he dies he asks Sister Paxton to pray for him out of fear of death thus exposing him as a hypocrite having forced his beliefs onto them while still having his own doubts that he could be wrong.