To directly answer your question: it is not. "Natural" sugar is no healthier than "refined" sugar, and sugar in fruits is no healthier than sugar in juice. Sugar molecules are sugar molecules, regardless of whether they are "natural" or "refined." There is no difference.
However, I believe the real question here is why the WHO is recommending one type of food over another, so I'll attempt to address this.
The sugar is the same, but (1) the rest of the food that you eat with the sugar is different, so (2) your overall diet is different, (3) which leads to different health effects.
(1) When you eat refined sugar you are typically not consuming nutrient-dense foods. A simple example is oranges vs. orange juice. Have you ever tried to eat three oranges? It's not easy. You have to chew a lot of pulp, which fills you up, and later on you may have bowel issues due to the large amount of fiber. These are natural mechanisms that help to prevent you from over-consuming oranges. However, if you instead squeeze these oranges, you get a glass of orange juice, which is easy to drink, and due to the lack of pulp it is easy to digest and does not fill you up.
(2) A healthy diet has carbs, protein, fats, fiber, water, vitamins, minerals, and other nutrients, and if you eat a balanced mix of fruits, vegetables, meats, grains, nuts, and/or other "natural" foods, you can get a pretty good mix of these. If you consume a large quantity of refined foods, you'll get a lot of sugar, salt, and fat, but not much else, so you get a lot of calories but don't make much progress in your overall nutrient needs. This has the dual effects of excess calories and nutrient deficiency. You're starving (for nutrients) and over-consuming (sugar, salt, and fat) at the same time.
(3) This unbalanced diet (heavy in sugar) leads to some health effects such as (a) excess weight gain, and (b) decreased insulin sensitivity.
(3a) Fructose is generally processed by the liver, and it does not trigger the "fullness" feeling like glucose and other foods, leading to excess calorie consumption and weight gain. This extra body fat is associated with negative health effects.
(3b) Insulin helps regulate blood sugar, but it can lose effectiveness, especially when blood sugar quickly and repeatedly rises to high levels. This is not just due to sugar, but starch and high glycemic index foods that easily break down into glucose. The amount matters, too. It's not just how fast the food gets converted to glucose but how much of it there is.
Table sugar (sucrose) and corn syrup (including high fructose corn syrup) have both glucose and fructose, so you'll probably see both effects if you include enough refined foods in your diet.
So, bottom line: refined foods have the same sugar chemicals, but the overall composition of the foods is skewed away from nutrients and toward sugar, which means the overall diet is out of balance, leading to over-consumption of calories, weight gain, and insulin resistance, which are associated with a number of health problems.
References:
[1] Maria Gadoy, "What's More Nutritious, Orange Juice Or An Orange? It's Complicated", January 22, 2015, NPR, https://www.npr.org/sections/thesalt/2015/01/22/378920980/for-more-nutrients-drink-oj-or-eat-an-orange-it-s-not-so-clear-cut
Interesting discussion about pros and cons of oranges vs. juice. Bottom line: cooking (pasteurizing) can release some nutrients better than fresh oranges, but juice has no fiber and does not fill you up.
[2] DiNicolantonio JJ, Berger A. Added sugars drive nutrient and energy deficit in obesity: a new paradigm. Open Heart 2016;3:e000469. doi: 10.1136/openhrt-2016-000469
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4975866/
"Not only do added sugars displace nutritionally superior foods in the diet, but they may also deplete nutrients from other foods that have been consumed, as well as from body stores, in order to enable their proper oxidation and liberate their calories as energy."
"Although edible, added sugars cannot be considered a ‘food’, nor can their consumption be equated to eating foods that contain natural amounts of sugar, but which also provide fibre, vitamins, minerals and other phytonutrients that combat oxidative stress produced by the small amounts of fructose present."
[3] George A Bray; How bad is fructose?, The American Journal of Clinical Nutrition, Volume 86, Issue 4, 1 October 2007, Pages 895–896, https://doi.org/10.1093/ajcn/86.4.895
"When ingested by itself, fructose is poorly absorbed from the gastrointestinal tract, and it is almost entirely cleared by the liver"
"Glucose stimulates insulin release from the isolated pancreas, but fructose does not."
"Fructose is metabolized, primarily in the liver, by phosphorylation on the 1-position, a process that bypasses the rate-limiting phosphofructokinase step (4). Hepatic metabolism of fructose thus favors lipogenesis, and it is not surprising that several studies have found changes in circulating lipids when subjects eat high-fructose diets"
[4] Peter J. Havel; Dietary Fructose: Implications for Dysregulation of Energy Homeostasis and Lipid/Carbohydrate Metabolism, Nutrition Reviews, Volume 63, Issue 5, 1 May 2005, Pages 133–157, https://doi.org/10.1111/j.1753-4887.2005.tb00132.x
"Compared with glucose, the hepatic metabolism of fructose favors lipogenesis, which may contribute to hyperlipidemia and obesity. Fructose does not increase insulin and leptin or suppress ghrelin, which suggests an endocrine mechanism by which it induces a positive energy balance."
[5] Boyd Swinburn, Gary Sacks, Eric Ravussin; Increased food energy supply is more than sufficient to explain the US epidemic of obesity, The American Journal of Clinical Nutrition, Volume 90, Issue 6, 1 December 2009, Pages 1453–1456, https://doi.org/10.3945/ajcn.2009.28595
"Increased energy intake appears to be more than sufficient to explain weight gain in the US population."
[6] Sam Z. Sun, Mark W. Empie; Fructose metabolism in humans – what isotopic tracer studies tell us, Nutrition & Metabolism 2012 9:89, October 2012.
https://doi.org/10.1186/1743-7075-9-89
Detailed account of fructose metabolism.
[7] Prediabetes & Insulin Resistance, National Institute of Diabetes and Digestive and Kidney Diseases, NIH. https://www.niddk.nih.gov/health-information/diabetes/overview/what-is-diabetes/prediabetes-insulin-resistance
"Although the exact causes of insulin resistance are not completely understood, scientists think the major contributors to insulin resistance are excess weight and physical inactivity."
