Mark Oppenhiemer writes in the New York Times:

In “Courting Disaster: How the C.I.A. Kept America Safe and How Barack Obama Is Inviting the Next Attack,” Mr. Thiessen, a practicing Roman Catholic, says that waterboarding suspected terrorists was not only useful and desirable, but permitted by the teachings of the Catholic Church.

This does not square, to put it mildly, with the common understanding of Catholic teaching. In the past month, as Mr. Thiessen went into book-promoting mode on TV and radio shows, Catholic bloggers and writers from across the political spectrum united to attack his views, and to defend their own: that waterboarding is torture, and that Roman Catholics are not supposed to do it.

Mr. Thiessen makes two basic arguments. First, he says that waterboarding, the simulated drowning used on Khalid Sheikh Mohammed, the chief planner of the Sept. 11 attacks, and others, is not torture. “I didn’t get into the Catholic theological stuff of it until I sat down to write the book,” Mr. Thiessen said in a phone interview. So when Mr. Bush asked him, in 2006, to write a speech explaining the C.I.A.’s interrogation program, Mr. Thiessen asked himself other kinds of questions.

Thiessen takes some premises of the Catholic catechism and runs with it:

The Catechism states, “the defense of the common good requires that an unjust aggressor be rendered unable to do harm,” and Catholic tradition accepts that this might involve killing. And, Mr. Thiessen writes: “If this principle applies to taking human life, it must certainly apply to coercive interrogation as well. A captured terrorist is an unjust aggressor who retains the power to kill many thousands by withholding information about planned attacks.”

To justify killing in self-defense, Catholics point to Thomas Aquinas’s principle of double-effect: the intended effect is to save your own life; killing is the unintended effect. By the same logic, Mr. Thiessen argues, “the intent of the interrogator is not to cause harm to the detainee; rather, it is to render the aggressor unable to cause harm to society.”

Andrew Sullivan says that Theissen was interviewed on EWTN but not challenged on this point:

Now I am not one to criticize Catholics who in good conscience dissent from the Magisterium on some topics, because I do so myself. I certainly do not deny that I am in conflict with the Magisterium on the question of homosexuality. This is not true of Marc Thiessen, as he is interviewed in an extremely supportive fashion by Raymond Arroyo, a Catholic media figure prominent enough to have been given the only English language interview with Pope Benedict XVI.

Sullivan points out that what Thiessen defends is an intrinsic evil as described by Catholic bishops.

the US Catholic Bishops have also made their position quite clear. From Dr. Stephen Colecchi, Director, Office of International Justice and Peace, Department of Justice, Peace and Human Development, United States Conference of Catholic Bishops:

"Torture is about the rights of victims, but it is also about who we are as a people. In a statement on Forming Consciences for Faithful Citizenship, issued in preparation for our recent national elections [2008], the bishops reminded Catholics that torture is 'intrinsically evil' and 'can never be justified.' There are some things we must never do. We must never take the lives of innocent people. We must never torture other human beings."

This is not a hedged statement. It is a categorical statement that what Thiessen is defending is, from a Catholic point of view, intrinsically evil and something that cannot be done under any circumstances.

One Catholic ethicist points out that Theissen is correct on one narrow point; Catholic teaching does not specifically mention waterboarding and therefore it is not specifically condemned. When asked what he would think if the Roman Catholic Church did name the specific torture techniquie, would that make what was done immoral? Thiessen says that it would not.

“On what competence would they do that?” Mr. Thiessen replied. “I don’t think the church would be competent to judge whether the way we did it was torture.”

“Perhaps,” he added, “they should clarify it. We were in the middle of a war, and there was no teaching on that. But the church only gives general moral guidance, and people of good faith have to interpret that guidance.”

So in the end, Thiessen assures us that the Church says torture is moral, but should they declare it immoral (which they have) it would not matter because the Church is not competent to rule torture immoral during time of war. Seems that for this Catholic, the Church's teaching is only useful when you agree with it.