Cut away the yellow and they should be OK. To keep animals away buy some moth balls and throw a handful around the plants. Animals don't like the scent. You will need to do this occasionally because the balls will melt.
Put a fence around the garden, and train the dog to go elsewhere. If the vegetables are forming, don't eat them.
I have a tomato plant and young pepper plant that dog pee has gotten on them. Can they be salvaged? They're still growing but when should i trust the veggies to be worth eating?