The comparisons made in this article and comments below seem to all but forget one major fact that completely changes everything. That is, Atomic bombs are NOT the same as carpet bombing say Tokyo. Why? RADIATION. If the major cities and sites of Japan suffered a disaster due conventional bombing The thinking would be – afterward we rebuild. You don't think that when your left with a radiation zone. So the theory that atomic bombs would have carried the same level of concern due to simply looking at leveled cities and that carpet bombing does the same as nukes is short sighted to say the least.
I was under the impression that the long-term effects of radiation and nuclear weapons weren't well known at the time of the Japanese surrender. If that's so, it is unlikely such concerns as you describe played much of a role.