They took Kyoto off the list because one of the men in command had spent time there, and decided to bomb Nagasaki instead.
Of course, there were a number of those in the administartion who really didn't like Christians in general. The real reason for the targeting will probably never be known.
Secretary of War Henry Stemson, a Skull and Bones man, took Kyoto off the list because of "its religious significance." Stemson then added the most Christian and most Catholic city in Japan to the list -- Nagasaki.