I have a sneaking suspicion that the situation in Afghanistan is a bit more complex than "because Islam".
Well, noone ever claims that religion is the only culprit.
The concept of "separation between the state and religion" was introduced a few hundred years ago by a philosopher John Locke and also made popular by Thomas Jefferson. Since then it has become a model that has been believed and applied by many nations in this world successfully.
It is quite the same concept with "trias politica" introduced by Montesquieu in 1748. It is a model which requires the strict separation of power into three branches: a legislature, an executive, and a judiciary. This model has been applied by many nations successfully. Why use a model that has been proven to be one of the cause of a failed state in the past ?
Why would anyone need to live under a constant threat, and subject to abuses by not believing a certain religion. Let alone it has its own court which is linked to a particular religion ?