Yes there will be a division between flavor and nutrition because people are starting to become wiser about preservatives, chemicals and GMO foods, and processed foods. People are going to start going for the more healthier foods and the processed foods will not last much longer as we know of it to be right now.
The best way to think of the current food landscape is as a triangle. Not the food pyramid that we learned about in elementary school, but as a three way competition between flavor, nutrition, and convenience. There are few foods that excel in all three of these areas. You can find nutritious and flavorful food, but it is not as easy (or cheap) to acquire as fast food, which is convenient and flavorful, but not nutritious. You can also find convenient and nutritious food like raw broccoli, but most people do not find that to be particularly flavorful. There is already a division between flavor and nutrition (with convenience playing an important part).
I find myself with nerve endings to my tongue imprinted to detect certain nutrients I find in food. Your taste buds are naturally designed to tell you what is good for and what is bad. If you can code your brain to detect the nutrients your body needs and ones that are just a waste than you can in fact find nutrients you are going for with just your taste buds. It maybe rough data but using it right would make something like raw vegetables taste better than cooked ones.
Artificial flavors can cause confusion and bad habits to us in childhood and stay with us until adulthood so be weary and don't be fooled by what is supposed to taste good and what is supposed to taste bad, when I was a child I hated sodas but I only began to like it when I wondered why everyone else liked it so kept trying it myself. The same went for fried food, in other words I was conditioned to feel junk food tasted good, you can condition yourself out of it if you have the willpower.
No, I don't believe science could ever do that, and we'll always associate certain flavors with certain nutrition in food. However, if it ever got the spot where it could be done, I would see it as a great thing. I simply don't see it happening while we have greater hurdles in science.
I do not believe there is, nor will there be in the future, a division between flavor and nutrition in food. All foods are healthy in moderation and in the right balance. This means it is okay for me to enjoy chocolate as long as I balance it out with health eating choices. I enjoy carrots just as much as unhealthy foods. Healthy foods can taste good, they shouldn't be thought of as lacking flavor because that simply is not true.