President Musharraf is beset in Pakistan by multiple woes, many of his own making. Just when he needs the support of the relatively secular middle classes to back his confrontation with religious extremists who support Taliban and Al Qaeda networks, he has alienated large numbers of middle of the road Pakistanis by trumping up charges against the nation’s chief justice. The fiasco led to large demonstrations by lawyers, doctors, and others disgruntled with the Musharraf regime. Now Mr. Musharraf has ordered a tactical retreat in respect of the chief justice, in hopes of focusing on the other front that has opened up against the jihadists.

Mr. Musharraf’s reluctance to take on his internal religious radical right was linked to his dual track policy of backing America while tolerating, or turning a blind eye to, the Taliban. His ability to pursue these mutually exclusive policies now appears exhausted. Relations between the Taliban and the army’s intelligence services run deep, though support for the Taliban among the Pakistani army is more geo-strategic than theological. It is conventional wisdom among Pakistani leaders that the country requires a friendly government in Kabul, as a hedge against India, and that once their interest in Al Qaeda is satiated, the Americans will abandon Pakistan, as we did following the expulsion of Soviet forces from Afghanistan.

Mr. Musharraf only released his military forces to confront Islamic extremists grouped around the jihadist Red Mosque in Islamabad after their provocations were more than he could bear. The successful siege of the mosque triggered anger among the religious extremists and renewed conflict in the mountainous areas along the border with Afghanistan. It is there that American intelligence officials have argued, with mounting intensity, that the Taliban and Al Qaeda have regrouped and flourished. On July 11, American intelligence services launched a public counter offensive. The CIA deputy director for intelligence, John A. Kringen, told a House committee that Al Qaeda appears “to be fairly well settled into the safe haven in the ungoverned spaces of Pakistan.”

Thomas Fingar, deputy director of national intelligence for analysis, said, “sooner or later, you have to quit permitting them [Al Qaeda] to have a safe haven there,” but warned that “there is some risk of turning a problem in northwest Pakistan into the problem of all of Pakistan.” The State Department was more reserved. One day after Mr. Kringen’s testimony, the assistant secretary for South and Central Asia, Richard A. Boucher, applauded Pakistan’s decision to move” troops into the region, putting up better checkpoints near the borders … [and] equipped the people there better.”

Mr. Boucher told a House subcommittee, “The government has now made clear to the tribes that all the foreign elements, the foreign militants … need to be expelled.” He announced new subsidies for Pakistan, to the tune of $100 million a year for the next five years for the development of the Federally Administered Tribal Areas, in addition to the $100 million a month already provided to Pakistan for monitoring the Pakistani-Afghan border. Additionally, Mr. Boucher said that Pakistan would also contribute a $100 million a year for the next 10 years for the development of the tribal region.

Enter Congress. In a June 1 letter, lawmakers Congressmen Lehtinen, a Florida Republican, and Lantos, a Democrat from the Coast, and Senator Biden, a Democrat of Delaware, urged Secretary Rice to press the Musharraf government “to commit to holding free and fair elections by the year’s end.” We’re all for it. But focusing on the human rights and pro-democracy points on the American-Pakistani agenda to the exclusion of everything else could prove disastrous, as it did in Iran. Hence this, or any, administration in Washington has its work cut out for itself. As Daniel Markey notes in the summer number of Foreign Affairs, (“A False Choice in Pakistan,”) “Washington’s choice is not between Musharraf and democracy, nor is it between Musharraf and radical militants. Rather, the choice is between an army chief (Musharraf or a successor) in a coalition with progressives and moderates and an army chief in league with other less appealing partners.”

A similar point is made in the July 23 number of the New Yorker by William Dalrymple, who quotes Jugnu Mohsin, publisher of Pakistan’s Friday Times: “The fall of Musharraf could well lead to the rise of violent political Islam. I certainly believe that no civilian government on its own can put that genie back in the bottle.” There are those of us who well remember the way the pell mell retreat into the Dark Ages in Iran was preceded by a long period of agitation over human rights, a period that ushered in a flight in the wrong direction. This is a history that needs to be kept in mind as policy is worked out on Pakistan, lest we be confronted with an Islamist victory in a country that possesses nuclear weapons.