Yes. The body does treat the energy from calories pretty much the same once they are consumed, but as we wrote in a recent news piece, calories from sugary soda are unique. They're much more easy to over-consume than calories from many other sources, and they can have unhealthy effects on the response of insulin and related hormones. And soda is well-established as the prime contributor to weight gain in the US - the theme of last year's PSA campaign from the New York City Department of Health (see below).
Should Coke be praised for its modest moves toward fighting obesity? Some may say "yes," yet the messages that all calories are the same and that everyone needs to "come together" to fight obesity seems a PR move aimed simply at deflecting growing criticism rather than a real effort to improve the health of kids and adults the world over. It is a company built on selling sugar water. To expect it to significantly veer toward health promotion would be little more than delusion.