I wonder what Pope Benedict XVI would have thought of John F Kennedy, the first Catholic president of the United States. Kennedy was a proud defender of the West against Soviet communism, while the new pope has equated the godless materialism of western freedom with Nazi and communist dictatorship.

Kennedy’s domestic politics, moreover, were based on a simple, remarkable assertion: “I believe in an America where the separation of church and state is absolute — where no Catholic prelate would tell the president (should he be Catholic) how to act . . . I believe in an America that is officially neither Catholic, Protestant nor Jewish.”

This statement of secularism by the most prominent Catholic figure on the planet at the time was seen as a blow against anti-Catholic prejudice. Today’s conservative Catholics would regard Kennedy’s statement as itself a product of anti-Catholic prejudice. For them the concept of a clear separation between religious faith and political practice has become suspect.

The Pope is quite explicit that all Catholics in public life must abide by the teachings of the church, especially on contentious moral issues. That’s why the then Cardinal Ratzinger was behind Vatican advice in the last presidential election, which argued that a politician who upholds the legal right to abortion (even if he personally disagrees with such a right) can be denied communion.

The same applied to such controversial issues as the right to die, same-sex marriage and stem cell research. The Pope once wrote about the seamless links between church and state in his native Bavaria: “I remember the joie de vivre of the local lads, firing their gun salutes — which was their way of welcoming Christ as a head of state, the head of state, the Lord of the world, present on their streets and in their village.”

Christ as head of state. It doesn’t get more explicit than that.

This is one reason why Ratzinger’s election has sent shockwaves across America. In the debate between reformists and traditionalists, there was no figure more polarising. Many of us Catholics thought he would be a big influence in the conclave. But after his fire-and-brimstone homily before the conclave on Monday, we assumed he would cede to a unifying, moderate candidate. How wrong we were.

When the news came through, my phone lit up with voices of panic, dread, fear and even sobs. A leading lay Catholic moderate, The Washington Post’s E J Dionne, described his response as “petrified”.

Here was a pontiff who had all but shut down real theological debate on America’s Catholic campuses. He had ruled out even a discussion of a married clergy in a country where a mere 500 priests were ordained last year for a Catholic population of 70m. His response to the sex abuse crisis was to protect and promote the most culpable official, Cardinal Bernard Law, and give him a prime spot in the mourning of John Paul II.

For good measure, he added: “I am personally convinced that the constant presence in the press of sins of Catholic priests, especially in the United States, is a planned campaign, as the percentage of these offences among priests is not higher than in other categories, and perhaps it is even lower.”

In a culture where women have reached near parity in the world of work and family, the Pope has declared that women should pursue either motherhood or virginity. Everything else is a surrender to “masculine” values.

In a society with a huge gay population, the Pope has declared that homosexuals have an innate tendency towards “intrinsic moral evil” and are therefore “objectively disordered”. He has also argued that the exercise of conscience is a sinful delusion if it doesn’t comport with church doctrine.

This shock, of course, is at the core of what the Pope is intent on providing. If his predecessor focused primarily on breaking the evil of communism, Benedict XVI is dedicated to confronting what he regards as the evil of democratic capitalism and permissive liberalism.

If this forces liberal Americans to leave the church, so be it. In 1970 Ratzinger wrote of the 18th-century church in Europe, reeling from the Enlightenment, that it was “a church reduced in size and diminished in social prestige, yet become fruitful from a new interior power, a power that released formative forces for the individual and for society”.

And this is his vision for the American Catholic church in the future: purged of wayward priests, lackadaisical believers and the liberal throngs that still cling to Catholicism’s basic tenets and rituals, while differing with it on social, cultural and sexual issues. A smaller, leaner, rump church, dominated by ultra-conservative lay groups such as Opus Dei is his goal.

It would be wrong to argue that this idea of the church is somehow radically new. But what is new is the way this theological ultra-conservatism has become fused with a political agenda in American politics.

A key part of Karl Rove’s attempt to build a new Republican majority has been a bid to bring conservative Catholics into the Republican fold. In America, Catholics have long tended to vote Democrat. But although American Catholics remain more liberal than most Americans, that has waned in the past few decades.

And the distinguishing characteristic that marks the new Republican Catholic voters is their higher rate of church attendance and their more conservative theology. By emphasising issues such as abortion, stem cell research, end-of-life decisions and homosexuality, the Republican leadership has pried enough Catholic swing voters into its camp to gain a small majority.

Benedict will only help that process along. That’s why the man who must have been celebrating more than many others last Tuesday was Karl Rove.

President Bush lobbied the Vatican last summer to pressure American Catholic bishops to back him more firmly on “culture of life” issues. Looming battles over court nominees, in which abortion will play a central role, will also keep the Pope in the American headlines.

In the raw Ratzinger could, of course, be a little counterproductive. The culture wars in America are already aflame, his elevation as Benedict XVI amounts to a barrel-full of petrol on the fire.

Those of us struggling to live as modern, open-minded Catholics can only hope the church isn’t burnt in the process.