I would look at this in the other direction, as it were.
The government did not come in and co-opt pure research. Instead, Albert Einstein wrote to Pres. Roosevelt suggesting that an atomic bomb was possible and that they US should build one (for fear that Nazi Germany would build one if they did not).
So the original use of the science was exactly what was contemplated by those scientists (except that it was against Japan, not Germany). The real change came when the understanding of nuclear physics was turned to civilian purposes such as generating electrical power.
I agree with pohnpei397's perspective. The "original intention" of atomic energy research -- at least of the huge research project in WWII -- was to develop a weapon. Only later does this project find major civilian applications.
This atomic energy example illustrates something very common: particularly in wartime (including the Cold War), modern militaries often push expensive research projects in order to develop more powerful techniques for offense and defense. Some of these techniques have huge and often wholly unexpected applicatons in peace time.
Airplanes, for example, were initially "toys" or strange artifacts that attempted to make possible the human dream of flight. With WWI, they were assigned and designed to better serve practical uses that they still serve today. If that's not a good example, here's another that might be better (but is certainly a lot more disturbing). In their war against entire populations of people, the Nazis found a use for the waste product of combustion engines, carbon monoxide; it was the gas used in most executions. They also adapted a pesticide (Zylon B, invented for vermin control) to kill those humans whom they also considered to be vermin.
This is one particular interest where pure science had drastic implications. Indeed, the use of atomic energy was a project with the idea of exploring new sources of energy output as well as the fundamental exploration of the nature of existence. Science in this instance became co-opted by the government and other forces which saw the potential for application within it. Many of the scientists who worked on the atomic bomb project were not doing so for the sake of nation as much as for the sake of science. They simply sought a solution for a problem that had perplexed and vexed them. The implications of this became quite profound when these scientists saw the death and destruction at Hiroshima and Nagasaki, and then saw the ushering in of the Cold War and the nuclear age. In this instance, the application of science became far beyond what was originally intended. Other forces had been able to gear science towards personal gain, which was far from the intended purpose.