What happened to the original "strong" class?

Friedrich Nietzsche, in On the Genealogy of Morality, sets his views on where our present state of morals comes from. In the beginning of humanity, the good were those people who exhibited all the characteristics of being “good,” such as health, power, strength, wealth, beauty, and things of that nature. The “bad” class had the opposites of these virtues. Nietzsche said the good acted this way because it was in their nature, and that their actions and decisions were not chosen upon, but acted that way because it was the only way the good could naturally act. The good did not think about the lower, “bad” class, as it was simply something that did not concern them. Eventually, over time, the “bad” people, or the slave class, got sick of their status and reversed the role of these classes, by stating that the good class in fact had a moral choice about their actions, and chose something that was harmful to the lower class, and made them an oppressive, moral evil. Nietzsche says that this idea of a choice between acting as the good or bad is a false choice, and it is solely natural to act either way, there is no moral decision making involved in the process. This essentially reversed the roles of the moral system into what we have today.

I find a problem with Nietzsche’s argument in that it seems to take away are perceived sense of free will and decision making. While it is true that some people are naturally stronger than others and some are weaker, it does not mean that they follow in accordance with their nature every time. If we are to be reduced to our base state of our instinct and act naturally according to whatever it is in our nature, then it seems as if we do have free will or any choice in the decision making process. This also destroys the whole sense of morality in our conscience today, which is what Nietzsche aims to do, as everyone perceives themselves as being moral, and having the ability to make conscience decisions about their actions. If Nietzsche’s ideas about the reversal of the classes and nature of the slave and the strong class, does this mean that all the Nietzsche-ian strong no longer exist if everyone believes that they have a moral choice, therefore making everyone part of the slave class? Or is it that even these strong at this point can act as the strong, they are just falsely believing in their choice and their inner strength leads them to act a certain way regardless of their perceived free will?