One can entertain the idea that the eventual outcome was ultimately better for all parties than the alternatives (though it's far from clear that's the case when the alternatives included "not playing hardball over unconditional surrender" and the scientists' favoured alternative of "demonstrate the bomb in a relatively benign manner") but the minutes of the meetings that made the decision quite explicitly discuss relative merits of targets in terms of the anticipated destructive effect on civilians, speaking favourably about wiping out Kyoto because of its high concentration of intellectuals before ultimately choosing Hiroshima over more obvious military targets because it "has the advantage of being such a size and with possible focusing from nearby mountains that a large fraction of the city may be destroyed" (and not really being militarily significant, it was largely undamaged). The notion that the surviving Japanese might ultimately be better off doesn't seem to have featured so highly in the decision-making calculus.
