Ali Abdullah Saleh, the nominal president of Yemen, arrived in New York City last week. The visit is uncomfortable, to say the least.

For the past year, Saleh and his government resisted a peaceful protest movement’s calls for his resignation; months of stalemated sit-ins and marches that filled the thoroughfares of Sanaa, Ibb, Ta’iz and Aden were punctuated by massacres of civilians and street battles between the military and tribal militias. In November, after seven months of stalling, Saleh finally signed a transition agreement negotiated by the Gulf Cooperation Council (GCC) and supported by the United States. Under the terms of the agreement, Saleh agreed to pass his powers (though not his title) to his vice president while a jiggered “unity government” is formed and harried elections are conducted to authorize a new executive. In exchange, Saleh received immunity from prosecution, which was recently formalized in Yemeni law.

But the crisis in Yemen is hardly over. Protests persist, calling for Saleh to be held accountable for the violence against protesters. The presidential election is still a month out, and the only candidate will be the vice president and acting executive, Abed Rabbo Mansour Hadi.

Saleh is, at best, an erstwhile ally of the United States and an autocrat deposed by his own people. At worst, he is a war criminal responsible for the deaths of hundreds of his citizens and decades of misrule. It is no wonder that many analysts, including Gregory D. Johnsen, Paul Pillar, Andrew Exum, Marc Lynch, Will Picard, the Wall Street Journal editorial page and the Yemeni-American Coalition for Change, among others, have complained about the Obama administration’s decision to admit him to the country, a choice that has only been made worse by poor public relations and a seemingly clueless State Department. Saleh’s visit to New York should provoke discomfort and frustration. But it is also the right course.

The outrage about Saleh’s visit to the United States is two-fold. First, there is the anger that Saleh should be granted immunity under the terms of the deal supported by the United States and now ratified by the Yemeni parliament. Second, there’s the indignation that the United States would accept him here for treatment after his conduct over the past year. Both are understandable responses. Critics raise the legitimate concern that the decision will continue to stoke anti-American sentiments among the prodemocracy protesters in an extremely volatile country.

The United States needs to do more to engage the Yemeni public, but Washington should not confuse Yemen for a democracy. Nor is it on the cusp of becoming one. Yemen’s revolution is far removed from the clean break from autocracy that Tunisia seems to be making, or even from the entropic cycle of protests, crack-downs and ultimately democratic elections in Egypt. The Yemeni revolution has only unseated Saleh—it has yet to change the government or its institutions, and this will not change with an election in February. There will still be no seat at the table for the nonaligned popular movements, who have made the most sacrifices and feel wronged by Saleh’s amnesty. An election does not a democracy make.

Saleh’s Continuing Influence

Throughout Saleh’s thirty-three-year rule, and even before, Yemen’s government has been a military autocracy riding atop a system of tribal power sharing and patronage with, at times, the superficial veneer of democracy. The removal of one man will not change this structure. The dominant forces in the parliament, the General People’s Congress (GPC) and the Islah Party, both have deep roots in Yemen’s tribal oligarchy. And though Saleh has been removed from the presidency, he has not been removed from the government—he retains the chairmanship of his political party and the GPC, and his sons and nephew command branches of the Yemeni military. After decades of skillfully manipulating Yemeni politics, it seems unlikely he will stop now, despite rumors that he is considering exile in Oman.

Political reform in Yemen will not occur overnight. Over the next two years, the government is slated to conduct a series of reforms, though it will almost certainly take longer. The military leadership will be shuffled. The constitution will be revised. New political parties will proliferate while old parties and centers of power will consolidate and adapt. Tribal organizations will jockey for power. The process of rebalancing the country’s political power will be long and at times very ugly, but it will be necessary for the reforms to be sustainable. The United States cannot ignore the fact that Saleh, both personally and through his relatives and proxies, will play a significant role in this reform. If Washington truly wants to help usher in democracy in Yemen, it must work with the breadth of Yemeni politics, including Saleh.

This arrangement is far from ideal. It is largely the result of the manifold faults of the GCC agreement, so far the only effect of which has been to grant Saleh immunity and set in motion the process that will formally remove him from the presidency. (Gregory Johnsen and Brian Whitaker were right to complain about the GCC deal’s faults from the beginning.) The United States’ unflagging commitment to the weak arrangement and the lack of credible alternative proposals was a critical failure of U.S. policy. But this is the agreement that was signed, not just by Saleh but by representatives of Yemeni opposition political parties as well.

The Right Choice

Immunity, no matter how distasteful, had to be part of the transition agreement in Yemen. Saleh never would have signed without it. Why would he, after the examples of Mubarak and Qaddafi? He had no incentive to step down into a domestic show trial or potential International Criminal Court indictment, not when he had demonstrated how easily he could stagnate the protest movement.

His strategy of delay was working. Over the summer and into the fall, the protest movement began to fragment as internal divisions and divergent interests became more pronounced. It seems likely that Saleh could have clung to power longer—and without the immunity clause, he probably would have. The GCC deal is a bad deal, but it was necessary to begin the process of introducing reforms. The United States should abide by it with the recognition that, as painful as it is to see justice denied to protesters who lost friends and loved ones to regime violence, it moves toward a Yemen that represents the interests of its people, so that events like those of the past year do not happen again.

Allowing Saleh to seek medical treatment in New York is a difficult choice, but ultimately the right one. The United States needs to play the long game, with the recognition that in the near-term Saleh will be more important in shaping reform in Yemen than the nonaligned populist protesters. The decision will provoke anger in Yemen and discomfort in Washington, but it is necessary to move toward sustainable democracy and complete Yemen’s revolution.

J. Dana Stuster is a researcher at the Center for a New American Security.