The nuke may have still hit, but he "repaired" the fault before it could sink half of California into the ocean. So there's some damage, sure, from the resulting earthquake but over all not as bas as it could have been. The nuke hit in a remote enough area of the fault for the resulting radiation to probably not be too big of a concern. (Or Superman could have taken care of that off camera.)
What's bizarre is that Luthor claims that with all of Superman's speed and powers he couldn't stop both missiles at once. Ummm... how does Luthor know this? And, YES HE CAN! Hell we SEE Superman speed around the earth at incredible enough speeds to REVERSE TIME! So I think he could have gotten both missiles pretty easily.
It also raises questions on "Returns" where Luthor is free because Superman didn't show up for court or "properly" arrest Luthor because he left for Krypton. I'm pretty sure a man who steals two nuclear missiles and launches them at the US isn't going to be showing up in a civil court where Superman needs to show up to bare witness. Luthor must have gotten himself a DAMN good lawyer to even GET a trial rather than the US government throwing Luthor in a hole somewhere and not looking back.