Hiroshima and Nagasaki were chosen simply because they were intact, utterly not out of any form of compassion.
. . . as it turned out, most of the Christians in Japan were in Hiroshima IIRC.
Exactly correct. Most everything else had been bombed into oblivion.
That, plus both cities were pretty involved in the Japanese war effort.
Unfortunately, Nagasaki was probably the highest % of Christians of anywhere in Japan.
But, oh well.