There is a way to get Jason out of the picture WITHOUT taking the predictable paths of killing him off or turning him into a villain or pulling some kind of 'cheat' plot device in which Jason is 'suddenly' not Superman's kid after all:
Have Lex inadvertently create red Kryptonite after lifting Superman's blood off the kryptonite stilletto chunks the medics pulled out of him in SR; he plans to clone Superman, but the DNA sequence is corrupted, so Lex abducts Jason to draw his blood to create patches - in doing so, Jason's exposure to red kryptonite has an adverse effect on his physiognomy, causing him to age at least two or three years a day. He become bait for a trap for Superman, who flies in to the rescue, as does Richard, separately; Richard is killed in the attempt, causing the public to lose faith in Superman and Lex to pass himself off as a hero with his own Super-clone. Superman decides to find a way to beat 'Bizarro' without his powers, but he's stopped by three mysterious super-powered individuals who at first come off as being homages to Zod & Co., but who turn out to be peacekeepers from the 30th century. (S:TAS, "New Kids In Town) They warn him that if he tries to fight Bizarro, he'll be killed, thus jeopardizing the course of future history and the lives of untold millions. Realizing he's going to do this no matter what, they give Superman a power ring with which he can take Bizarro hand-to-hand, but Bizarro has grown more powerful by the day - the result of his adrenaline overloading his solar-battery biochemistry - critically injures one of the 'visitors' and yanks the ring right off Superman's finger in the climax, ready to crush him till Jason flies in and sends Bizarro - who's gone critical - into the clouds where Bizarro explodes; the shockwave hits now-30-year-old Jason, carrying antibodies created from Bizarro's supercharged remains into his system, restoring his aging process to normal rate (Byrne's MOS). Realizing that he can no more fit in in the world now than he did when was a five-year-old asthmatic - and that with one of the 'visitors' down the group's going to need an extra hand - Jason takes his father's power ring, says an emotional goodbye to his mother, and takes off for the 30th century with the others. (Superboy & The Legion Of Superheroes)
Of course, this would require Routh to play FOUR roles, but if they could get him to stop impersonating Reeve and do his own thing (as in the screen test with Clark and Lois), you win half the battle right there.