I think that one of the purposes of Soaphead Church's letter is to emphasize how there are some examples of evil and malevolence in the world that cannot be eradicated.

We mistook violence for passion, indolence for leisure, and thought recklessness was freedom

Morrison uses Soaphead Church's letter to explore how some of these forces cannot find redemption, even in the presence of the divine.  The letter, itself, is far from clear.  In a traditional letter to the divine, one would conventionally express some type of fundamental regret and remorse.  The hope would be the one would lose their ego in the face of the divine.  

This is not the case in Soaphead Church's letter.  The lack of coherency in the letter and lack of admission for wrong in the letter is Morrison's way of inverting this traditional understanding.  The letter serves as a way to show how Soaphead Church embodies hypocrisy and a lack of authentic embrace of individual responsibility.  Moments in the letter such as comparing himself to God for being able to grant Pecola's wish as well as the idea that he can "work miracles" are representative of how little honesty there is in the letter.  The purpose of Soaphead Church's letter reflects how the order of things does not eradicate evil and that some of its forms exist.  While there is sadness, pain and suffering in the world, evil exists.  When the dog is found dead, Soaphead Church is asleep, as if nothing is wrong.  The letter to God highlights the condition of being in which evil exists and a lack of self- reformation is a part of it.