Her sucrose argument made me wonder because I do understand that refined sugar is unhealthy and is much better when part of a whole food.
Sugar is really sugar refined or not. When broken down and absorbed there is really no difference on effects in the body. Where the differences really come in between "junk foods" and whole food sugar sources are the fibers in the whole foods slow sugar absorption so there are not the big spikes. And the whole foods also provide nutrients such as B vitamins, magnesium and chromium that are required for carbohydrate metabolism, but can be depleted by over consumption of sugar sources not containing these nutrients.
Does FOS/Inulin as a supplement have any issues having been removed from its original whole food?
No, there is not an issue since it does not really work in a synergistic effect with other compounds in the foods.