Consequentialism, in a nutshell, says that it is acceptable to do something horrible as long as its for the greater good. Such as dropping the atomic bombs on cities filled with thousands of elderly, women, children, and non-combatant men. The Church has made it clear that such is incompatible with Christian morality. To be Catholic, to base one's moral compass on the Church's guidance, is to concede that fact no matter how difficult.
In explaining this, however, the Catholic apologist must be careful. One of the pitfalls of apologetics, and why I generally hesitate to delve into that branch of Christian ministry, is its own version of consequentialist tactics for winning theological arguments. This can be seen by some who rightly argue for the clear teachings of the Catholic Church, while then turning around and doing so in ways incompatible with moral, honest, grace-filled instruction.
For instance, the facts. Being right about morals doesn't give the right to twist facts, inflate events, ignore inconvenient arguments, or worse, bear false witness or falsely accuse. It should not involved sweeping condemnation or impugning the morals of those with whom we disagree. It should not be buying into silly theories or conspiracy nonsense without damn good evidence to back it up. Thus, it's OK to say Truman (and also Roosevelt, don't forget) was wrong to OK the bombings. But we need not add to it every wild, harebrained theory that Truman was really part of some vast, anti-Catholic conspiracy to murder Catholics in Nagasaki, that he knew Japan only wanted peace, love and John Lennon songs but just wanted to slaughter babies, that Truman molested teddy bears, or anything else. It's enough to stay with the facts as known.
It also does well to avoid polemical history to justify the stance. Not only does it run into the danger of suggesting, however subtly, that if there really was a utilitarian reason for the bombings then it would be OK, but it can be wrong. The idea that every thinking person knew the bombings were wrong since Japan merely wanted peace and all the signs were disregarded is a very, very biased interpretation of the events. It fails to take into account the lack of contemporary (c. August 1, 1945) documentation that suggests peace was right around the corner, fails to take into account any potential biases on the part of those who later condemned the bombings (while, of course, emphasizing the bias of those who support them), and generally ignores the growing evidence that Japan was anything but ready to capitulate on the eve of the attacks (this last brought out by the increased pressure on Japan in recent years to fess up to its own atrocities in the war).
In short, it's enough to point to the teaching of the Church on the subject. It's enough to say that there could have been an alternative. A real, positive alternative. Not one that could be as morally suspect as dropping the bombs. It also avoids the idea that the justification for the teachings rests on highly partistan reading of the historical data. And it certainly avoids the potential pitfall of the 'sword of the Lord' approach to apologetics: that I am so the mouthpiece of the living God, that his commandments (like call no one fool, don't bear false witness, judge not, and others) no longer apply to me. Once those begin to crop up, ironically, the teaching being advanced becomes swept up in the maelstrom of charge and counter charge, and fair minded people seeking the Truth are confronted with two arguments, both of which appear to be flawed.