Calories in v calories out is absolute in terms of weight loss/gain, but that's just a quantitative measure, not a qualitative one. For instance, the famed "Twinkies at a Caloric Deficit" diet will cause you to lose weight, but not in any sort of good way, and will do all sorts of terrible things to your health, not the least of which is deprivation of important micro and macro nutrients.

Sugar isn't inherently "bad", but the way most people consume it is. High sugar foods, in essence, have very poor bang for your caloric buck.