I think "completely different" is overstating it, the money quote from the article you linked is “the liver doesn’t know whether it came from fruit or not”.

Naturally occurring sugar is just as bad, but has some other ingredients deemed to have positive impact. The analogy here would be opposing the claim that smoking is bad for you with the statement that some cigarettes can contain menthol or eucalyptus, which are known to have soothing effects and pleasant odors, and therefore are "completely different".

But back to sugar. The usual pro-sugar argument with naturally occurring sugars involves vitamins and nutrients. Unless you have a severe case of vitamin deficiency, your body does not need extra supply of those vitamins, at least doesn't need them urgently enough to justify sugar as a delivery mechanism.

Nutrients can be obtained from zero-sugar green leafy vegetables - watercress and kale tend to be the bomb as far as nutrient load.

Also "naturally occurring" is a misnomer by itself - modern commercially available fruit has been bred to have longer shelf lives and higher contents of sugar to appeal to general public.