It looked like they were going to be martyrs, but al-Sistani snatched away their victory while saving their lives. This preserved (and perhaps even strengthened) their organization; but their political primacy was pre-empted byal-Sistani.
Did the U.S .win or lose in Najaf? The U.S. lost in two ways. It further alienated the Iraqis, so that neither the U.S. nor its client administration have any credibility on the street. It also lost the opportunity for a smashing military victory that might have won the November election for Bush and intimidated Shia militants enough to keep them quiet while the U.S. developed and implemented a new program for the Shia areas of the country.
But the U.S. also won two things from al-Sistani's intervention. First, it was relieved of a terrible choice: either withdrawing without dislodging al Sadr (which would have been a monumental victory for al Sadr and would have led to liberated areas throughout the South of Iraq); or smashing the shrine and creating Islam-wide outrage that could have led to an immediate insurrection throughout the country. So the U.S. lived to try another strategy, which they would not have had the chance to do if al-Sistani had not intervened.
Second, al-Sistani's pre-emption provided a template for the new strategy that the U.S. adopted soon afterward. His truce-making provided an orderly process by which the Iraqi police (trained and controlled by the U.S.) took official control of old Najaf. Their authority is guaranteed by the legitimacy of al-Sistani, and therefore they have not had to face a challenge by militant Sadrists or other insurgents (though the police themselves may not remain loyal to the U.S., a process we have seen elsewhere already). For the U.S., this created the vision of parallel developments in other cities: an alliance with "moderates" that legitimated the Iraqi police while effectively removing the militants from the public life of the city.
The New U.S. Strategy.
The new U.S. strategy, then, is targeted at the cities where the guerrillas and their clerical leadership dominate, notably Falluja, Samarra, Tal Afar, and Sadr City (though there are several others which have not been in the news lately). The U.S. method is to negotiate with the clerics, offering extensive reconstruction aid in exchange for calling off the insurgency and perhaps delivering the guerrilla fighters over to the U.S. (They call this negotiating with the moderates to split with the militants.)
If they can get an agreement, then the U.S. marches into town and arrests at least some of the guerrillas, using informants to determine whom to target. If the guerrillas resist arrest, the U.S. annihilates them and the areas they take refuge in. If they melt into the population, then the Iraqi police and National Guard take up stations within the city to enforce the rule of a re-established local government. American troops outside the city maintain the capacity to intervene against any effort to challenge the police or National Guard.
To force an agreement, the U.S. threatens both economic and military attacks on the city as a whole. Part of the plan is to use brutal air power that can annihilate buildings or whole city blocks in an effort to convince residents and leaders that the cost of resistance is simply too high. The underlying assumption is that the "moderates" will eventually choose to negotiate rather than see their city destroyed. As one marine officer in Falluja told Washington Post reporter Rajiv Chadrasekaran, the goal is "to split the city, to get the good people of the city on one side and the terrorists on the other."
The new plan is designed to achieve two goals. First, the U.S. hopes to drastically reduce the number of attacks on U.S. convoys and bases outside the cities. These attacks are planned within the cities, the weapons used are stockpiled there, and the guerrillas are protected from detection by their civilian identities as members of local communities. By demobilizing, arresting, or killing the guerillas, the new plan holds the potential to drastically reduce the direct attacks on U.S. forces.