Section 31 was portrayed as having extraordinary powers so that its methods could be portrayed as being a genuine choice between life and death. Section 31 means life while ideals mean dying for them. The very possibility that living morally is a means to a fuller, happier and longer life is foreclosed as unimaginable. This says more about the writers as people than it does about the human condition.
But even if so, such foolish premises make the storyline irrelevant as a commentary on the human condition. There is no eternal empire, no monolithic ruling class, no military threat so grave that genocide is both justified and possible. By the way, the importance and relevance of simple physical possibility is sadly underrated. In practice, any storyline playing with genocide is bascially arguing that there is some dreadful enemy in real life against whom "we" must exercise merciless violence, in self defense of course. All the absurd powers imputed to the SF versions are mere expressions of hysteria about the RL foes.
In DS9, the genocide on the founders is heavily justified - so much so that the arguments to the contrary are easily nullified.
That's because the entire situation was painted in such cartoonish black/white colors - uncompromising absolutes.
I can think of another similar situation - in nuBSG, genocide by biological weapon on the cylons is, again, heavily justified, for the same reason. The cylons/colonial situation is portrayed in such stark black/white colors.
But in real life? I cannot think of any situation along the same lines.
The best known example would be Hirohima/Nagasaki, and the moral justification for their atomic bombing is lacking:
- the inhabitants of the 2 cities has little influence or military might themselves; they had little responsibility for the previous events of the war;
- the war would have ended in a few months without the atom bomb use (a fact allied commanders were aware of);
- the allies could make an atom bomb every ~3 months; as such, they could afford to at least start with a military target, demonstrating their new power;
As for other real life genocides and their "justifications" - well, let's just say they make the Hiroshima and Nagasaki excuses look extremely well by comparison.