A faction divergent would be indeed a supreme faction, because 1. They are not controllable by any means not even among each other, and 2. The faction could not be joined by choice, but by divergence only.
These two factors are reasons for other factions to fight this one obviously superior faction, no balance could be held upright.
It is a very serious problem for others to deal with divergence. And that is not only the case in this fantasy sci-fi but a real life issue, that people who do not seem to fit in anywhere become outsiders. But not only that. Due to the fact that they are uncontrollable, people tend to be afraid of them and for that hate them.
So in my opinion there should be no separation between the factions, but jobs. For example young people could join dauntless in order to learn how to stand up for themselves, protect others and conquer their fears, then they could go on and learn the virtues of the other factions one after another and the test should give them hints for what they should work on, in order to become a whole humanbeing. The life in each faction for a few years should give everyone of them a clear understanding of the pilosophy of each calling. By this method all people would learn to be divergent and the problem of one faction controlling another would not be necessary. Also the witchhunt for divergents should not come into question any longer.
The problem I guess is that his story seems to imply that people are just born the way they are and not become the way they are due to certain personal life experience. And the ideology behind is that peoples fates is determined by their genes, which is a myth. Because genes, while they give certain outlines are not by any means restricting to certain preset way of life or character. In other words there is no such thing as talent, there is only training and mastery of certain qualities, virtues and abilities. For example the ability of a so called divergent to distinguish between a simulation, hallucination or a dream and reality is a skill that can be learned by anybody who trains it, either on purpose or through certain personal experience that motivated them to do.
If this story is telling anything then in my opinion it is that a real whole human being is divergent and should not be stuck in one of the preset ideologies and their inherent qualities and virtues, by excluding others. The fact that Four has this tatoo on his back is exactly supporting my point, because while he is not tested as divergent, he indeed is divergent also, or at least knows that this is the way things should be. He wants to be truthful, courageous, intelligent, selfless and kind. And this can be achieved by intermarrying, friendship, exchange and collecting all the personal life experience that is needed individually.