You can't ignore it. It is in the movie. They specifically put it in there for a reason. To establish that Eisntein's theory of relativity exists in the film's established logic. Jor El probably had some way of seing into time to get his son up to speed on the trip to earth and to acclimate into it's timeline. But he definately died many thousands of years ago in earth's history. You apparently have blinders on and refuse to see the major plot hole that Singer used when establishing STM and S2 into his films backstory. You should go write for the guy and come up with all sorts of plot holes for his next films and call it "vague history".
Best way I can state it is Superman Returns is like Batman Forever. Even though there is a different actor playing him, and a cimpletely different city, there is still some actors that are the same. The event's of Batman 89 and Batman Returns happened. Batman killed the joker, and he had an affair with returns catwoman, as stated by the dialog in that film. Same damn thing. So the rules that were set up and applied in Batman 89 apply to Forever, even though it is technically vague history too. Those lines delivered by Chase Meridian and Kilmer's lines to Robin are meant to tie the movies in, and the rules.
Even James Bond films up to the last one acknowledges everything that happened in previous films as the backstory of each new film. So you can say that Pierce Brosnan's Bond wife died, it just happend to be in an almost 30 year old film with another actor playing him. But the character shares the same past. His James Bond was the Bond on the space station in Moonraker. Any injury from any of the back films is an injury he still has effecting him, even if it happened to another actor in another film playing him.
Let's watch the man say it:
http://www.youtube.com/watch?v=qB6fjVpAyM8&mode=related&search=