CAIRO — The revolution that began here two years ago with calls for justice and freedom has become a rout by Islamist forces that have racked up victory upon victory at the polls.

But within Egypt and across the region, the real source of fears that the country is hurtling toward theocracy lies in an unlikely place: the ancient stone corridors of al-Azhar, a Cairo mosque and university complex that long has been known as a respected beacon of moderation.