PRESIDENT OBAMA’S eloquent endorsement on Friday of a planned Islamic cultural center near the World Trade Center, followed by his apparent retreat the next day, was just one of many paradoxes at the heart of the increasingly impassioned controversy.

We have seen the Anti-Defamation League, an organization dedicated to ending “unjust and unfair discrimination,” seek to discriminate against American Muslims. We have seen Newt Gingrich depict the organization behind the center — the Cordoba Initiative, which is dedicated to “improving Muslim-West relations” and interfaith dialogue — as a “deliberately insulting” and triumphalist force attempting to built a monument to Muslim victory near the site of the twin towers.

Most laughably, we have seen politicians like Rick Lazio, a Republican candidate for New York governor, question whether Imam Feisal Abdul Rauf, the principal figure behind the project, might have links to “radical organizations.”

The problem with such claims goes far beyond the fate of a mosque in downtown Manhattan. They show a dangerously inadequate understanding of the many divisions, complexities and nuances within the Islamic world — a failure that hugely hampers Western efforts to fight violent Islamic extremism and to reconcile Americans with peaceful adherents of the world’s second-largest religion.

Most of us are perfectly capable of making distinctions within the Christian world. The fact that someone is a Boston Roman Catholic doesn’t mean he’s in league with Irish Republican Army bomb makers, just as not all Orthodox Christians have ties to Serbian war criminals or Southern Baptists to the murderers of abortion doctors.

Yet many of our leaders have a tendency to see the Islamic world as a single, terrifying monolith. Had the George W. Bush administration been more aware of the irreconcilable differences between the Salafist jihadists of Al Qaeda and the secular Baathists of Saddam Hussein’s Iraq, the United States might never have blundered into a disastrous war, and instead kept its focus on rebuilding post-Taliban Afghanistan while the hearts and minds of the Afghans were still open to persuasion.

Feisal Abdul Rauf of the Cordoba Initiative is one of America’s leading thinkers of Sufism, the mystical form of Islam, which in terms of goals and outlook couldn’t be farther from the violent Wahhabism of the jihadists. His videos and sermons preach love, the remembrance of God (or “zikr”) and reconciliation. His slightly New Agey rhetoric makes him sound, for better or worse, like a Muslim Deepak Chopra. But in the eyes of Osama bin Laden and the Taliban, he is an infidel-loving, grave-worshiping apostate; they no doubt regard him as a legitimate target for assassination.

For such moderate, pluralistic Sufi imams are the front line against the most violent forms of Islam. In the most radical parts of the Muslim world, Sufi leaders risk their lives for their tolerant beliefs, every bit as bravely as American troops on the ground in Baghdad and Kabul do. Sufism is the most pluralistic incarnation of Islam — accessible to the learned and the ignorant, the faithful and nonbelievers — and is thus a uniquely valuable bridge between East and West.

The great Sufi saints like the 13th-century Persian poet Rumi held that all existence and all religions were one, all manifestations of the same divine reality. What was important was not the empty ritual of the mosque, church, synagogue or temple, but the striving to understand that divinity can best be reached through the gateway of the human heart: that we all can find paradise within us, if we know where to look. In some ways Sufism, with its emphasis on love rather than judgment, represents the New Testament of Islam.

While the West remains blind to the divisions and distinctions within Islam, the challenge posed by the Sufi vision of the faith is not lost on the extremists. This was shown most violently on July 2, when the Pakistani Taliban organized a double-suicide bombing of the Data Darbar, the largest Sufi shrine in Lahore,Pakistan’s second-largest city. The attack took place on a Thursday night, when the shrine was at its busiest; 42 people were killed and 175 were injured.

Symbolically, however, the most devastating Taliban attack occurred last spring at the shrine of the 17th-century poet-saint Rahman Baba, at the foot of the Khyber Pass in northwest Pakistan. For centuries, the complex has been a place for musicians and poets to gather, and Rahman Baba’s Sufi verses had long made him the national poet of the Pashtuns living on both sides of the Afghanistan-Pakistan border. “I am a lover, and I deal in love,” wrote the saint. “Sow flowers,/ so your surroundings become a garden./ Don’t sow thorns; for they will prick your feet./ We are all one body./ Whoever tortures another, wounds himself.”

THEN, about a decade ago, a Saudi-financed religious school, or madrasa, was built at the end of the path leading to the shrine. Soon its students took it upon themselves to halt what they see as the un-Islamic practices of Rahman Baba’s admirers. When I last visited it in 2003, the shrine-keeper, Tila Mohammed, described how young students were coming regularly to complain that his shrine was a center of idolatry and immorality.

“My family have been singing here for generations,” he told me. “But now these madrasa students come and tell us that what we do is wrong. They tell women to stay at home. This used to be a place where people came to get peace of mind. Now when they come here they just encounter more problems.”

Then, one morning in early March 2009, a group of Pakistani Taliban arrived at the shrine before dawn and placed dynamite packages around the squinches supporting the shrine’s dome. In the ensuing explosion, the mausoleum was destroyed, but at least nobody was killed. The Pakistani Taliban quickly took credit, blaming the shrine’s administrators for allowing women to pray and seek healing there.

The good news is that Sufis, though mild, are also resilient. While the Wahhabis have become dominant in northern Pakistan ever since we chose to finance their fight against the Soviets in Afghanistan, things are different in Sindh Province in southern Pakistan. Sufis are putting up a strong resistance on behalf of the pluralist, composite culture that emerged in the course of a thousand years of cohabitation between Hinduism and Islam.

Last year, when I visited a shrine of the saint Lal Shahbaz Qalandar in the town of Sehwan, I was astonished by the strength and the openness of the feelings against those puritan mullahs who criticize as heresy all homage to Sufi saints.

“I feel that it is my duty to protect both the Sufi saints, just as they have protected me,” one woman told me. “Today in our Pakistan there are so many of these mullahs and Wahhabis who say that to pay respect to the saints in their shrines is heresy. Those hypocrites! They sit there reading their law books and arguing about how long their beards should be, and fail to listen to the true message of the prophet.”

There are many like her; indeed, until recently Sufism was the dominant form of Islam in South Asia. And her point of view shows why the West would do well to view Sufis as natural allies against the extremists. A 2007 study by the RAND Corporation found that Sufis’ open, intellectual interpretation of Islam makes them ideal “partners in the effort to combat Islamist extremism.”

Sufism is an entirely indigenous, deeply rooted resistance movement against violent Islamic radicalism. Whether it can be harnessed to a political end is not clear. But the least we can do is to encourage the Sufis in our own societies. Men like Imam Feisal Abdul Rauf should be embraced as vital allies, and we should have only contempt for those who, through ignorance or political calculation, attempt to conflate them with the extremists.

William Dalrymple is the author, most recently, of “Nine Lives: In Search of the Sacred in Modern India.”