Since ignoring the cat has worked before I'd try doing that again. It sounds like your son will continue to wake up as the cat tries but once the cat learns you're not going to let her out your son will once more sleep thru the night.
I'd also try using the techniques that are used to help babies learn to get back to sleep. Leave him in his crib, let him fuss a little, going to him to reassure him but leave him in the crib. If the cat yowls and is scary you may want to do more of course.
How long did it take the cat to learn when you've ignored him in the past? Another idea is that perhaps the cat has a urinary tract infection which has caused her to do this again.
Cats, just as people, age and need to urinate more often. Does he have a litter box? If not, using one might help. It says something good for the cat if he's wanting out and not urinating in the house without a litter box.
I also suggest that you could consult with a vet. Now we also have vets who specialize in animal emotional issues. My daughter works for Banfield, The Pet Hospital in administration. She has praised Banfield's many services.
My brother takes his dogs to Companion Vetenarians because their rates are lower than some and he receives good service.
When I call for an appointment I'd specify the reason and ask if they have someone on staff who addresses this sort of issue.
I think Petco also has vets on staff. Many Petsmart stores have a Banfield office in their building.