Basically, Paul was sacrificed to save Peter and Gene.
John was going down with that ship too.
Maybe not hit, prob shelved. And you shelve a guy like John, you may as well hit him. Because you're taking away his identity and effectively killing him.
And then you've got a problem on your hands. As Paul found out.
MORGAN: Why didn't you fight him at the park if you wanted to? I'm not goin' now, I'm eatin' my snack. CHUCKIE: Morgan, Let's go. MORGAN: I'm serious Chuckie, I ain't goin'. WILL: So don't go.