The wrongness of European Crusades
If the Christians from Europe wanted to honor Jerusalem as a holy city, that's one thing. But the Crusaders regard Muslims as enemies of God, and they are violent and ruthless. They don't just coexist (not that it was an option; the Muslims were not really happy with European Catholics in the 12th century). The novel shows 12th century Crusades to be unfounded religious wars designed to make Muslims into permanent enemies.
The Israeli-Palestinian Conflict
One unspoken theme is that the Israeli-Palestinian conflict from our modern globe is very similar to the past. This story about Saladin's victory is obviously not the final battle that ever gets fought in Jerusalem. The city is highly contested even today. This novel shows that the real problem in Jerusalem is that Islamic and Judeo-Christian cultures have historically regarded each other with hatred and disgust.
Political instability and the Arab spring
Saladin won an important battle for the Muslim world, regaining Jerusalem. So the Khalifa makes him king of Syria and Egypt. That is not a picture of political stability. By flippantly rewarding entire nations as Saladin's reward, the implication is that such extreme reactions don't lead to political stability. Based on this novel's depiction, the government in those nations should have been managed better.
