Discussions about the long-term effects of using the atomic bomb were taking place alongside the actual development of it. The military were not usually the ones leading this discussion, though; it tended to be civilian policymakers and scientists who did. So for example the Secretary of War, Henry Stimson, spent a lot of time talking about the atomic bomb as something that would require a totally new system of international governance, and saw it as a technology with massive implications for the nascent United Nations organization. Minutes of a meeting of the Interim Committee in May 1945 record: "The Secretary expressed the view, a view shared by General Marshall, that this project should not be considered simply in terms of military weapons, but as a new relationship of man to the universe." So that's a pretty strong statement that this was not merely a new weapon but some kind of revolutionary force.

Stimson and others were also aware, and discussed with Truman, that the postwar technology was likely to improve dramatically: the weapons would be more powerful, they would be developed by multiple countries if left to its natural path, and new innovations in things like rocketry would make them even more effective and easier to use. They foresaw that unrestricted warfare of this sort would lead to great peril. As Stimson told Truman in the latter's first long briefing on the bomb in April 1945: "The world in its present state of moral advancement compared with its technical development would be eventually at the mercy of such a weapon. In other words, modern civilization might be completely destroyed."

So these questions were discussed at the highest levels, especially towards the end of the project. The overall goal was to set up some kind of framework for control in the postwar, something other than a secret arms race between the USA and USSR (and others). These "international control" schemes obviously failed for a lot of reasons.

Martin Sherwin's A World Destroyed has a lot on this subject; Alice Kimball-Smith's A Peril and a Hope covers the push for international control well.