I believe it was a tactical mistake on Clark's part to have Superman confront Luthor originally at the end of the Pilot. By doing so he allowed Luthor to see his cards. First, Luthor denies that he had anything to do with Antoniette Baine's death, but as soon as he sees that Superman isn't going to hurt him or take him to the authorities with these unsubstanciated claims, he shows his true colors by saying one of my favorite of his lines: "Let the games begin."
This scene reminds me of a preview of what's to come in the "Never-Ending Battle" and the confrontation scene there.
