This would fall into the philosophical argument of the trolley problem I think. Is it morally superior to intervene and save 5 people who will die, if it means your actions directly cause the death of 1 other person who would have lived?
It's a thought provoking question. But, for this Utilitarian Humanist anyway, the greatest good for the greatest number would not lead to genocide in any sense. I do not see how genocide stems from that. I do know definitively however that religious believes are the cause of a not-insignificant number of genocides. So I very much disagree that religion prioritizes the individuals well being and prevents genocide.
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When trying to maximize the greatest good for the greatest number, how can you justify leaving 10 million people with mediocre lives when you can give 9 million great lives?
Can you share some of the religious genocides? I'd like to learn about them.