Section 31 is a vigilante organization, then, like the Justice League. They're powerful and not responsible to anyone in power.
Yet S31 is evil but the JL is "good". Is being unanswerable really so terrible even if lives are saved by their actions?
And is it possible to commit genocide against the Founders? If they're in the Great Link, aren't they just one individual? Genocide can't be committed against one person. Though I suppose they could be considered the last of their kind, and killing them would be causing their extinction.