Nagasaki was the one area of Japan that was heavily Christian. The United States had the opportunity to bomb military or government targets. Instead they chose to bomb civilians.
The Hiroshima bomb was dropped on the southwest corner of the Japanese Second General Army HQ, a base of over 20,000 soldiers, and which directed the defense of Kyushu, which was the site of the planned U.S. invasion in the autumn. Hiroshima was the principal port city supplying this army.
The "Nagasaki" bomb was actually assigned to Kokura Arsenal, the largest intact purely military target in Japan. The unescorted bomber was unable to bomb Kokura Arsenal due to fighter opposition, and ended up dropping the bomb on the only target it could reach with its remaining fuel (Nagasaki was its tertiary target).
So the U.S. actually targeted high value military targets, not just "bombing civilians".