Hi!
The choice really depends on your mood. We like both, but they are completely different in many different ways. Our opinion only, we prefer Cape May Cafe, but both are great, and sometimes we're in the mood for Whispering Canyon Cafe. some thoughts:
Whispering Canyon:
gives us a chance to hop to Wilderness Lodge, which is just awesome!
the meal has more of a "show" feel to it, if you like the interactivity. E.g., the servers are "in character," there's hootin and hollerin, and of course the horse race as you mentioned. I assume if you let the cast members know about your concern about your child, they'll be sensitive enough to find a way to include her.
the food is southwestern all american barbecue style, the famous skillet is great and feeds us just fine. could be heavy if you're not in the mood, though.
Cape May Cafe:
gives us a chance to hop to the Epcot resorts area (where we like to stay anyway). Theming is Atlantic coast, marina ... we love it. and after dinner, you can stroll the boardwalk ... or go to Epcot for Illuminations
no "show" or interactivity so much at dinner (there are character breakfasts there I think).
food is seafood! preference only, but we like seafood a little better than meat (but we love both) ... and CMC has meat too.
CMC also has a nice little kids buffet area (chicken fingers, etc).
and the dessert table is nice.
Again, depends on your mood.
hope this helps.