Harry Walker / MCT via Getty Images Oklahoma Governor Mary Fallin warns that Washington "cannot simply ignore our laws or the will of the people.”

Military leaders like to cite the importance of unity of command, where everyone knows who is boss. Unfortunately for that vital martial guideline, each state’s National Guard reports to both its governor, and — through the Pentagon — to the President.

That dual-headed command structure has led to a second confederation of seven southern states that is refusing to issue ID cards that entitle same-sex spouses of military members to claim benefits. After the Supreme Court struck down the federal Defense of Marriage Act in June, the Pentagon said it would recognize same-sex marriages and issue military ID cards to same-sex spouses, including members of the National Guard.

But some states, citing state laws barring such unions, said their National Guard same-sex couples would have to visit a federal facility to get their spousal ID cards that entitle them to benefits, ranging from base access to commissary privileges to health care. In some states, such federal sites are hours away.

Florida, Georgia, Indiana, Louisiana, Mississippi, Oklahoma, South Carolina, Texas and West Virginia initially balked, although Indiana and West Virginia have backed down. Florida and South Carolina decided to make it tougher on everyone, by deciding that anyone seeking a spousal ID would have to visit a federal site to get one. “Our adjutant general has responsibility to meet the policies and governing authority of both state and federal levels,” says South Carolina National Guard Major Cynthia King. “If they are in conflict, he must ensure both are being met.” A spokesman for the Florida National Guard told the Miami Herald that “we want to ensure that everyone is treated equally and all Florida National Guard members get their benefits in the same place.”

Georgia is simply sending gay military couples to federal facilities. “The State of Georgia does not recognize same-sex marriages and is not authorizing the Georgia National Guard to process the applications for same-sex married benefits at state facilities,” the Georgia Department of Defense says. “Any personnel seeking to apply for same-sex married benefits will be referred to federal facilities.”

It’s somewhat analogous to the “separate but equal” doctrine that created separate drinking fountains for blacks and whites during the Jim Crow era. Such a clash “is a pretty rare thing,” says Lawrence Korb, who served as the Pentagon’s top personnel chief during the Reagan Administration. State National Guard units are under their governors’ command unless they are federalized, as many were for the wars in Afghanistan and Iraq. But if they are not federalized, “technically” they are not under the Pentagon’s control, he says. Yet because the Pentagon provides 96% of the Guard’s budget, it retains the upper hand. “The Air National Guard,” Korb says, “doesn’t pay for those F-16s they’re flying.”

Hagel has been resolute on the subject. “Whether they are responding to natural disasters here at home in their states or fighting in Afghanistan, our National Guardsmen all wear the uniform of the United States of America,” he said. “They – and their families – are entitled to all the benefits and respect accorded to all of our military men and women.”

But Oklahoma Republican Gov. Mary Fallin basically told Hagel to go pound sand. “Oklahoma law is clear. The state of Oklahoma does not recognize same sex marriages, nor does it confer marriage benefits to same sex couples,” she said in a statement last week endorsing a decision to send gay couples to federal facilities for ID cards. That decision, she added, “protects the integrity of our state Constitution and sends a message to the federal government that they cannot simply ignore our laws or the will of the people.”

A spokesman for one of the recalcitrant states says his National Guard is just following the governor’s order, which is based on a law passed by the state’s voters several years ago limiting marriage to a woman and a man. “You can debate it all you want,” says the official, who asked that his state not be named, “but that’s what’s happening here, and I don’t see it changing.”

Advocates of same-sex unions aren’t retreating. “All service members and their families serving in the National Guard deserve to be treated equally, no matter what state of our nation they serve in,” says Stephen Peters, president of the American Military Partner Association, a nonprofit group dedicated to the families of gay service personnel. “It’s clear from the response of some state officials that further action by the secretary of defense must be taken to correct this unfortunate resistance to diversity.”

Pentagon officials have threatened further action, without specifying just what that might be. Korb, now a senior fellow at the Center for American Progress, isn’t sure any additional action is needed. He suggests that the decision of two states to back down indicates “they have spoken to their lawyers,” and he expects the others to do the same, eventually.

Eugene Fidell, former president of the National Institute of Military Justice and a lecturer at Yale Law School, says if push comes to shove, the law is on Hagel’s side. “Basically, when federal and state law conflict, and the federal law is within Congress’s power to enact,” he says, “the federal law trumps state law under the Supremacy Clause of the Constitution.”