In the unlikely event of a deal, the Iranian regime is highly likely to trumpet such an agreement as proof that the West does not care about the Iranian opposition and that the regime's hold is rock solid. That claim could resonate in Iran and disillusion democrats about the West -- not good in general but particularly not good if the democrats ever come to power. Sixty years ago, the United States, for geostrategic reasons, supported an autocratic Iranian government (that of the shah) against a popular movement (led by Mohammad Mossadegh). The result was not good for the U.S. image around the world and was disastrous for Iran. Before shoring up another autocratic Iranian government for geostrategic gain, we should pause to weigh the risks and benefits, especially if we are not completely sure the Iranian regime will stick to the deal.
For the United States to stay silent on human rights out of fear of how such statements might affect negotiations is to confuse ends and means. Negotiations are one way to advance U.S. interests, not an interest in themselves. A more democratic Iran that is more respectful of human rights would serve the interests of both Americans and Iranians. Such a reality would put the two countries on a path toward resolving not only the nuclear crisis but also state support for terrorism and interference in the internal affairs of Arab countries such as Lebanon and Iraq. A democratic Iran would become a normal state rather than a revolutionary cause.
I would be the first to say that I do not see much evidence that Iranian democrats will come to power any time soon. But I know someone who thinks this is a realistic prospect, and his name is Supreme Leader Ayatollah Ali Khamenei. He frequently warns about the danger of a velvet revolution -- a quick overthrow of the Islamic Republic by a popular movement of youth, women, and intellectuals stirred up by Western media like the BBC. Presumably Khamenei knows something about Iranian politics and Iranian public opinion.
It is not the place of outsiders to determine what kind of government Iran should have, but we are not indifferent to the outcome of the power struggles in Tehran. Even while strenuously objecting to what it saw as a "regime change" policy by the Bush administration, the New York Times wrote in an editorial on April 11, 2006, "The best hope for avoiding a nuclear-armed Iran lies in encouraging political evolution there over the next decade." That was true six years ago, and it is true today.