Well, Lex killed his father for himself, too. He couldn't let Lionel have that power over him. The way I picture it working out is that Lex sticks with the psychotic break story, realizing that Clark knows the truth. And Clark accepts the psychotic break story, realizing that Lex knows he knows the truth. The lack of outward admission allows them to go forward together, battered and more bitter perhaps, but still together.