Watching Fat Man Little Boy and Gojira back to back was an interesting experience, in the extreme contrast of both the style and moral positions.
Contrary, the scientist in Gojira took full responsibility for the weapon he created. He could have used a similar excuse, that he just discovered the method for developing the device, and was not liable for any uses it may be put to. Instead, he accepted ultimate responsibility and destroyed all knowledge of his research, including himself, so it could never be duplicated and used for more sinister things after taking down the monster. Unlike the american scientists, who could disassociate themselves from blame in their minds, he felt fully accountable for anything that it might be used for, even when out of his hands.
However, if I were in the position of the american scientists, I feel as though it might not be quite as clear-cut as it seems from a broader outside view, like many things. By putting it on the executives who have the final decision of what application your research will have, you can easily personally relieve yourself of blame. The scientists probably realized at some level that what they were doing went against their morality, but rather than struggle with cognitive dissonance, they rationalized it to themselves so they wouldn't feel guilty. I can see how it would be exciting to be involved in something so monumental. In Fat Man Little Boy their awe at the massive mushroom cloud produced from the first major test demonstrates this; they were so caught up in the project that even seeing its power and destructive capability they were thrilled instead of horrified.
I can find other ways to rationalize it as well--if you turned down the opportunity because you were morally opposed to it, someone else would easily fill your place, and nothing would be different. Scientists, like many holders of technical jobs, are fairly replaceable. Someone will step up to the job, if not you, the next guy. And if it's going to happen regardless, it's almost like a cop-out to let someone else take your place just so you don't have to feel guilty. What if you could do a better job, make it safer?
It's scary that it is easy to think like this, because you are absolutely responsible for how your research is utilized. To not thoroughly consider the possible drawbacks and impacts is just careless. Unfortunately, many destructive things have been created by well meaning people. However, intent still doesn't factor into the outcome. And especially for the Manhattan Project, the scientists knew full well what they were developing and what it would be used for.
If I were a scientist and asked to take part in research that had weapons applications, I would like to say that I would absolutely decline. It isn't something that I could ever feel comfortable or good about doing. If it was my only career option, I would rather choose something that felt like I was affecting the world in a positive way to offset the people who chose the other path.