While I can't answer why Seth thinks the cleansing rain aspect undermines it, I totally agree it's not necessary to the main theme. For one thing, it's not central to Judah or anything that has been written about his character.
So are you telling me that every scene has to be central to Judah? If so, I don't agree with that point because not every scene shot in any film has to be about the protagonist or any other central characters per se. Obviously, the scene was shot for dramatic effect to emphazise the cleansing of mankind due to the death of Jesus and the washing of his blood from the rain.
Crawdaddy