Well what did they expect the US to do then. Simply lay siege to Japan for a few years? That would have been cruel to orders of magnitude more people than the two Bombs were.
Why do you assume that this would necessarily be the case? I'd have to do some research to confirm this, but I don't think Japan's agricultural base was incapable of feeding its own population. True -- it had to import natural resources from all over the Pacific Rim in order to maintain a modern state and a major military force. But eliminating a nation's affluence by laying siege to it is hardly "cruel" in any sense -- especially if the vast majority of that nation's citizens are delusional enough to believe that it is somehow a worthwhile price to pay for their obstinate "honor" in defending their country.