Sunshine Seasons is a CS that has a lot of different & healthier options - that's in The Land Pavillion in Epcot Future World. I usually get the steamed white rice with vegetables from there. My kids like the chicken leg platter.
At MK, there's Columbia Harbor House CS - not sure how much healthier it is, but different choices abound. They have tuna sandwiches (to die for) on multi grain bread, broccoli slaw sandwiches, and then the traditional fried seafood baskets (fish & chips or shrimp). There's also a baked potato cart outside of CHH, and you can bring that into CHH to eat.
In Epcot's World Showcase try CS Tangierine Cafe in Morocco. They have a great vegetarian sampler platter that includes hummus & bread, tabouleh, couscous, marinated olives, lentil salad & more. Very light & refreshing on a hot day, but enough food to fill you up (or share).