I feel like Cooper has to lose Janey-E and Sonny Jim. He isn't her husband or his father, he's known them for like a week, and given how fiercely Janey-E stands by Dougie in all his slowness, it seems like she was very much in love with him. It would be really weird if Cooper stuck around with them.
Killing them off would be the easiest way to tie that subplot up.
He might genetically be Sonny Jim's father depending on how the Dopplegangers work.