There are two things here. One is whether MacArthur really opposed the use of the atomic bombs against Japan, and why he would have said that (after the fact). The other is his views on the Korean War and future uses of atomic bombs.

With World War II, MacArthur was part of a group of high-level military men who later said that they had doubts about the use of the atomic bomb (Eisenhower and Leahy are also in this group). There isn't any evidence that they voiced this doubts at the time; rather, their voicing of opposition seems to have been a postwar activity direct tied into the over-attribution of the end of the war to the atomic bomb (and not conventional actions) and the subsequent fear that reliance on nuclear weapons would mean deep cuts to the conventional military budget (which were not entirely unfounded — Truman cut the defense budget to lows in the immediate postwar that the US has not seen since the Korean War) would all lead to a much smaller US military posture than they desired. They were, it is worth noting, backed up by the US Strategic Bombing Survey, which concluded that the bombs were not really necessary to end the war.

At its heart, this argument was not a moral one — they were not arguing that the destruction of Japanese cities or lives was a problem, just that in the case of the atomic bombs it was unnecessary, because they had already beaten Japan through the conventional destruction of Japanese cities and military infrastructure. Their problem with the bomb was not, in other words, that of regarding it as a "taboo" — it was a very different sort of objection than those that argued that the weapons were immoral, weapons of slaughter, etc.

Consequently it is not really paradoxical that they also essentially supported the idea of atomic weapons as not being inherently "special." They saw them as perhaps a more efficient form of munition and destruction, but not a morally different form. Consequently when it came to things like the Korean War, if the atomic bomb was the weapon that would achieve the best military ends, they had no real qualms.

The really interesting thing is that many of those who supported the bombings of Japan opposed the use of atomic weapons more broadly, and believed in their "special" nature. Truman was very much of this turn of mind: he saw the atomic bomb as something quite different from other conventional weapons, as something that could not only not be used lightly, but not even trusted to the military. In the postwar, he frequently espoused the view private that the bomb did pose moral and ethical hazards that would restrict its possible use, whatever the military advice might be.

The reason this all feels surprising to a modern reader is that our politics of the bomb have shifted dramatically over the course of the Cold War. I like to bring this up when talking to audiences about the politics of the atomic bomb: they are contextual, and not obvious.

On the construction of the "specialness" of the bomb, see Michael Gordin, Five Days in August, and also Nina Tannenwald, The nuclear taboo.