The so-called “friendly fire” incident this weekend, in which US forces killed more than two dozen Pakistani soldiers at a border post near Afghanistan, is only the latest in a long string of incidents that have inflamed US-Pakistan relations. But this one may be the most serious of all. Already, Pakistan has closed two critical border crossings that provide about half of the American and NATO resupply effort for the war in Afghanistan, and Pakistani officials are saying that the closing is permanent this time. (They’ve closed them previously, only to reopen them after a cooling-off period.)

The closing may yet be reversed, but it’s a sign of Pakistan’s ability to undermine or even shut down the US war effort. (It’s not really possible to supply US forces by using the so-called northern route through Russia and the ’Stans, not is it possible to airlift supplies such as fuel, heavy machinery, and construction equipment in sufficient quantities.) As always, Pakistan has the United States over a barrel.

Worse, the Pakistan government is threatening to boycott the December 5 international conference on Afghanistan, at which 1,000 delegates from fifty countries are scheduled to convene in Germany to discuss plans to wind down the war. As everyone who’s paying attention knows, winding down the war—removing 30,000 American troops in 2012 and taking out the rest by 2014—means getting Pakistan and its cat’s-paw, the Taliban, to the bargaining table. If Pakistan doesn’t play, it’s game over.

The most intelligent comment on the crisis comes from Vali Nasr, a regional expert who served as a consultant to the late Af-Pak coordinator Richard Holbrooke. Nasr told the New York Times that there is not one but two policies toward Afghanistan, the first one being the White House and State Department policy of seeking a political accord, and the second being the Department of Defense and the military command policy of killing the enemy. “It’s a case of the tail wagging the dog. U.S. commanders on the ground are deciding U.S.-Pakistan policy.” That may exaggerate the point slightly, since the White House is in charge, but it does point to the fact that if a war can’t be won militarily, it’s probably best not to let the military try to win it.

Crabby comments from US politicians, including Senators John Kyl and Dick Durbin, badly miss the point. Rather than “get tough” with Pakistan, the United States has to recognize that when and if the war ends Pakistan will be the dominant player in Afghanistan. So the United States needs Pakistan’s help. At the same time, the United States has to led a diplomatic surge to get Russia, India and Iran to rein in their warlike allies among the anti-Karzai Northern Alliance, so that some sort of deal can be struck to stabilize Afghanistan after the United States leaves. Otherwise, the country will be plunged into a full-scale civil war such as the one that raged in the early 1990s after the USSR withdrew and before the Taliban took over to end the bloodshed.