Several things come to mind:
1. Something hurt her while eating at her regular bowl, and now she associates that bowl or area with fear and pain. I don't think that it hurts to eat in general since she ate some of your food, it's just THAT particular area.
Maybe try offering her the same cat food, but on a saucer and in a different location.
2. Her acting scared and scratching your son makes me think that she's having some sort of pain. How soft was your cereal? It could be something hurting her teeth, now that I think about it. Maybe some tinsel was in her food and is now stuck in her teeth? It's possible that soft cereal and eggs didn't hurt, but her regular food does.
3. Her scratching your son when he picked her up, though... maybe he squeezed a sore area? Maybe try touching her sides kind of gently and see if she reacts. Cats hide pain REAL well, though, so just look for any discreet signs of discomfort, like if she starts watching your hand when you get to a certain area.
On a side note, I found with my Charlie (who passed a few weeks ago) that the best kitty litter to use was the Breeze Cat pellets with a pee mat underneath. The other kind hurt his joints to dig in, but I didn't realize it until I paid attention and saw that he wasn't covering his movements. Pine was WAY too strongly scented for him, and the World's Best kind was expensive and broke down too quickly. He was 16 1/2 when he passed.
As an added bonus, thanks to the pee mats I now can see that my other cat (Mojo, also 16 1/2) is dealing with bloody urine... an issue I would have never seen in regular litter.