I agree with the first answer.  However, if you need to argue that MacArthur could have done something, here's what you can say.

MacArthur had a huge amount of prestige with the American people.  I imagine he had more prestige at that point than the President did.  So MacArthur could have used that.  He could have said that he would resign his command if the President did not offer a conditional peace as outlined in the first answer.  He could have threatened to make his opinion public.

This is essentially the sort of thing he did in the Korean War, so he could have done it in WWII if he had wanted to.

In a word, nothing.  This topic has come up fairly often in recent days, and the consensus seems to be the same: the decision to drop the atomic bomb was made because of a desire for revenge and to shorten the war.  The decision was made at the Presidential level, even before we had the bomb developed for testing.  So MacArthur, while he was the Supreme Allied Commander in the Pacific and had a great amount of respect and influence on military matters, would not, in my opinion, have been able to stop the bomb from being used.  He may have been able to influence the timing of its use, but that's about it.  He later admitted himself that he had not even been consulted about the use of the weapon.

That being said, MacArthur did have a military opinion on it.  He believed it was militarily unnecessary.  As we did not accept an unconditional surrender of Japan, but a conditional one where the Emperor would retain his position but not his power, he felt that concession might have prompted the Japanese to stop fighting without the use of the bomb.  Unfortunately, we'll never know.