Operation Paperclip wasn't to protect general run-of-the-mill Nazis, it was to protect the scientists and engineers who had done all that research that made Nazi Germany the juggernaut that it was. It wasn't to protect architects of the Holocaust, High Command, etc., it was to protect scientific research that was extremely valuable, including nuclear secrets, no matter how it was compiled. Most of those scientists weren't really Nazis, they were just German scientists, doing what scientists do, for the benefit of their nation. It was an unsavory, but necessary post-war step to preserve their important, and extremely valuable research.
But we still tried, and executed many of the real Nazi leadership. Punishing the true shitheads, while confiscating whatever good came out of their atrocities seems like the best outcome of a war.