Ok so to answer wtf is going on here....Daniel wants Bandy's land for his pipeline. He tries making him a lowball offer which Daniel is used to men taking due to their shortsighted greed. Bandy gives zero fucks and will only give him the land if he is baptized by Eli's church. So far throughout the movie we see Daniel as a man with only serving motives so of course he finally agrees to do it. There's a cool shot that happens now where the camera follows Daniel down the aisle up on the stage next to Eli. He drops down on his knees and there is a closeup of Daniel. The bright light shines through the giant cross on the wall down on Daniel's oil slicked hair. He's going through the motions trying to put on a good show reciting the lines Eli yells at him hoping it will be over soon. Eli is not going to make it easy. He wants a little payback for earlier in the movie when Daniel slapped him up and threw him in the mud. Louder and louder he yells at him forcing Daniel to be humiliated in front of the congregation. Now for a brief moment, for the first time in the movie, Daniel breaks. "Ive abandoned my child! Ive abandoned my child! Ive abandoned my boy!" He sounds, looks, and feels nakedly sincere. His guilt for sending away his kid cannot be masked by the absolute distaste he has for the confession he is being subjected to. This adds critical depth to his character. He may not be just a self-serving hypocrite. The audience now has a reason to root for Daniel. This only lasts for a few seconds and then Daniel goes back to putting on a show. I think it was cut out of the youtube clip I posted but after Daniel gets slapped up, he stands up and shakes Eli's hand and whispers something into his ear. We can't hear it, but Eli has a nervous look on his face. This sets up the final scene of the movie perfectly.
I'm not really good at articulating my thoughts lol, but there's probably some good analysis online that you can find if you're really interested.