If it were a dog every single person here (almost) would say 'Get it put down before it hurts someone else'.
I don't particularly believe you can change an animals basic instincts once it's developed them and started to act on them, whether it be chicken, dog, cat, whatever even people who spend their entire lives in and out of prison.
By far the simplest thing, though heartbreaking for your family and especially your son, is to get a different rooster. Explain to him why his chicken has to go, although he might be more keen to keep his chicken and get rid of his sister - boys ! You could simply have an accident in the coop, for a four year old that might be an easier way to explain things.
If you can't catch him in the daytime, get him at night in the coop when it's dark. If you can't bring yourself to do the deed there and then, find someone who will do it for you.
You don't need to eat him, have a funeral, bury him and plant a tree on top, then your son will know where his chicken went.
Retraining is something you should want to do if you find it interesting, not something you should be forced to do to protect your family.
Roosters are easy to come by, there's people giving them away constantly.