You can plan for every situtation you can think of - but critters often come up with ones you don't think of. It never would have occurred to me either that a chick would fit through such a small hole. Sounds like you have done everything you can to secure the momma and remaining chick. My sympathies again on your loss.
As for chasing off the cat, try squirting it with water (a hose or a spray bottle) or water with vinegar in it. Do you know if the cat is someone's pet? If it is, I would definitely notify them of the deaths it caused - while they may not chose to keep the cat inside, they should be aware of what it is doing. If it is a stray, your options may be more limited.
