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Suppose that the qualitative difference is between bearable and unbearable, in other words things that are over o below the pain tolerance. A pain just below pain tolerance when experienced for a small quantity of time will remain bearable; however, if it is prolonged for lots of time it will become unbearable because human patience is limited. So, even if we give importance to qualitative differences, we can still choose to avoid torture and your scenario, without going against our intuitions, or be incoherent. Now, let's assume that the time will be quite short (5 second for example), in this case I think it is really better to let billions of people suffer 5 second of bearable pain than to let one person suffer 5 second of unbearable pain. After all, people can stand a bearable pain by definition. However, pain tolerance is subjective and in real life we don't know exactly where the threshold is in every person, so we can prefer, as heuristic rule, the option with less people involved when the pains are similar to each other (maybe we have evolved some system to make such approximations, a sort of threshold insensitivity).