Well Cloud did ask Vincent if sins are ever forgiven. I think that one of the big points in the movie is that Cloud is having trouble letting go of the past, along with his guilt over Aeirths fate. In the movie there is a wolf in places such as the church, and the cliff near Midgar where the Buster Sword is stuck into the ground. I believe that this represents his guilt. Before He goes to the Forgotten City, Cloud tells Tifa that he isn't able to help anyone. Then after Aeirth appears and tells him that it's time for him to forgive himself, he seems become stronger. I don't know much about religion however I think in Christianity a baptism signifies a rebirth. Cloud wakes up in the spring and it seems like he is ready to move on and not live in the past any longer. I think they may have taken some inspiration from that idea of rebirth and cleansing to symbolize that. At least that is what I think.