Some Muslims complain that stoning — along with other traditional penalties like whipping and the amputation of hands — is too often sensationalized in the West to smear the reputation of Islam generally. Most of these severe punishments are carried out by the Taliban and other radicals who, many Islamic scholars say, have little real knowledge of Islamic law. Stoning is a legal punishment in only a handful of Muslim countries — in addition to Iran, they include Saudi Arabia, Somalia, Sudan, Pakistan and Nigeria, but it is very rarely put to use.
Stoning is not prescribed by the Koran. The punishment is rooted in Islamic legal traditions, known as hadiths, that designate it as the penalty for adultery. While the penalty may seem savage to Western eyes, scholars say it is consistent with the values of Arabian society at the time of Muhammad, Islam’s founding prophet. . . .
But Islamic law requires very strict conditions for a stoning sentence: four male eyewitnesses must attest to having seen the sexual act and their accounts must match in all details, or else they can be subject to criminal penalties, said Aron Zysow, a specialist on Islamic law at Princeton University. Some scholars even argue that the stoning penalty is meant more as a symbolic warning against misbehavior than as a punishment to be taken literally.
The New York Times article also notes that stoning is not an exclusively religious practice, finding mention in many other ancient religious faiths.
Iranian lawyers who have been involved in such cases say that as many as 100 stonings have been carried out since the  revolution, but that the practice was becoming less common.
Between 2006 and 2008 at least six stonings took place, all of them in secret, said Hadi Ghaemi, the director of the International Campaign for Human Rights in Iran.
The opposite trends seem to be present in Taliban controlled parts of Afghanistan for stonings and other harsh punishments for trivial offenses are becoming common in cases such as the recent stoning of an eloping couple.
I don't think that it is inappropriate to condemn the fact that harsh corporal punishments are carried out under the banner of Islamic law.
I also think that many Islamic leaders in the places where these practices are carried out don't understand how far these practices put then beyond the "Moral Event Horizon" in the mass media narrative that guides Western democratic politics. The natural response to an account of this kind of punishment is to assume that everyone complicit in it is evil and deserves to be exterminated. This isn't the right response, but it takes extraordinary effort and a commitment to a particular set of values to overcome this instinct.