I'm frustrated by the common critical interpretation that "There Will Be Blood" is about the struggle between commerce and religion. In my opinion, this interpretation of the film's premise attempts to shoehorn it into a conventional structure that does not fit the film, and elevates the importance of the Eli Sunday, the Paul Dano character, while minimizing other characters who are of equal significance.
The narrative premise of "There Will Be Blood," is that Plainview, the Day-Lewis character, advances and protects his interests by attacking potential adversaries with a mercilessness that outstrips the capacity of those enemies to do him real harm. The film is about who Plainview presents himself as, who he sees himself as, and who he really is, and his dealings with Eli Sunday are a piece of that, the same as the disposition of a man fraudulently claiming to be Plainview's brother, and Plainview's vicious dealings with the man from Standard Oil, who attempts to buy out Plainview's stake in the area.
The film's much talked-about final scene is only an escalated version of the resolution of the other story threads, where the audience's identification with Plainview is ruptured as he presses his triumphs further than he needs to.
The central relationship of the film is Plainview's relationship with his adopted son, H.W. His emotional connection to the boy is a raw nerve for him, and this is illustrated clearly in the dealings with both Sunday and with the Standard Oil man, who attempt to use Plainview's connection to the boy to their advantage and end up inciting Plainview's rage.
The irony of the film, and Anderson's final judgment on Plainview, is that, through his cold and unbending nature, he transforms the only person he loves into the only adversary that can destroy him. The last scene between Plainview and Sunday is only a postscript to the confrontation in which H.W. breaks Plainview, illustrating that the experience has left Plainview no less vindictive and dangerous than before.
That being the case, it's not Day-Lewis who Anderson indulges, but Dano, whose character has more screen time than he ought to. Maybe Anderson felt that giving Dano more screen time added to the impact of the final scene, or maybe he just liked watching Dano's entertaining performance. Whatever the reason, the prominence of the Eli Sunday character obscures the real point of the narrative.