Were there any pilots that refused (or politely declined) to take part in the operations of "Fat Man" and "Little Boy," knowing the destruction these would cause? Similarly, were there any scientists or officials who resigned from or opted not to take part in the Manhattan Project, or any subsequent projects to create ever more destructive variants of the atom and hydrogen bombs?
Were there any pilots that declined to carry out the atomic bombing of Hiroshima and Nagasaki? The answer is no.
Then Lt. Colonel Paul W. Tibbets, who retired a Brigadier General, was put in charge of the newly formed 509th Composite Group of the Army Air Corps in September, 1944 (activated in December, 1944). He was a successful bomber pilot / leader and was recommended to Major General Uzal Ent, who was responsible for getting the atomic bombs dropped on targets, by Dwight Eisenhower himself.
Tibbets was given complete authority by Uzal to appropriate, transport and make needed alterations, etc. of the planes to be used. He also was allowed to pick and train the flight crews for the group--as well as the missions themselves.
Tibbets was the only member of the 509th who knew in advance what the missions would be, though it is likely others guessed as the time drew near. In preparation for the missions, Tibbets developed a dramatic diving turn for the bomber that he insisted all pilots of the group adapt and practice.
The idea behind the plane--and crew--stressing move was to create immediate speed to put as much distance as possible between the B-29 Super Fortress and the impact point of the bomb after the drop. All crews were required by Tibbets to have practiced the drop a minimum of 50 times.
All of the personnel associated with the 509th were well-trained and as best as I have been able to determine, all were excited to participate as well.
All crews had completed a minimum of 17 practice missions over Japan, dropping 10,000 lb. special "pumpkin" bombs, roughly the size and shape of the atomic bombs. All crews also participated in a minimum of 12 actual bombing missions just prior to the real events as well.
Tibbets, as the person responsible for picking mission crews, picked himself for the Hiroshima mission and Major Charles Sweeney for the second.
Just before take-off Tibbets gathered his crew together for a meeting. Without revealing exactly what they were going to do, he told them the mission was extremely dangerous. He also said anyone who wanted out would be allowed to do so without any question or recrimination. Everyone stayed. Only after being airborne were the crew advised about the mission.
The same was the case for the second mission.
This questions "asks a negative" so it is impossible to answer with absolute certainty, but I would highly doubt there was any hesitation among the air crews.
The B-29 crews were all elite crews who were highly expert and highly committed to the war effort. These men had already been fire bombing Tokyo and cities in Okinawa, so I doubt they had any qualms about killing Japanese civilians.
At the time, none of the current stigma over nuclear weapons existed. All they knew is that it was a powerful bomb. Of what the effects would be, they had no specific knowledge beyond what the missions required.
The Pacific war in general was a very brutal one, and both sides almost never took prisoners. The Japanese perpetrated gruesome tortures on any wounded they found left alive and frequently left the mutilated bodies where they knew Americans would find them. Our soldiers had ZERO sympathy for the Japanese and were doing the maximum to kill as many as they could. If some big blockbuster bomb worked, so much the better as far as they were concerned.