He knew what he was doing. In fact, being head of the Manhatten Project, he was one of only a handfull of people who did know exactly what they were building and how horriffic it would be.
"I was only following orders" wasn't a valid defense at Nuremburg, and quite rightly, it shouldn't be used by anyone, ever. We can't have one rule for America, and another for the rest of the world.... Oh, wait. :/