From what I remember of the prequel comic he left on his own without even saying goodbye (either personally or publicly) and just left. There was a little more justification to Kal-El leaving (there were some scientists that produced evidence that Krypton still existed...which was faked by Luthor BTW). Lois figures out he left without telling her when (a month after people begin wondering where is Suoerman) Lois breaks her arm in a fall to prevent getting caught during a stakeout.

CLARK: No. I'm just worried I'm a jinx.
JONATHAN: A jinx?
CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me.
-"Contact" (You're not her jinx, you're her blessing.)