Do you honestly think that the Popes didn't believe they were the Hand of God on Earth?
I fear you underestimate the corruption inherent to most organised religious systems. Or do you think Indulgences were a wholly moral idea?
Its funny, but religion is often just an excuse for hatred. Hatred that started with tit for tat theft of land, or differences of opinion. Most of the "religious" strife in the world boils down to pure human belligerence. Northern Ireland, Israel, India/Pakistan...... its got very little to do with religion. People just come to broad sweeping conclusions. Two neighbouring nations that hate each other? Must be religion. Two nations that are squabbling over the same patch of land? Must be religion. Two political groups that can't abide one another? Must be religion.
You know even if you took religion out of the equation, people would still find another excuse. Race, religion, caste, class, humans are always looking for ways to justify their hatred of the alien.
Furthermore, if religion worked as intended then 98% of the world's religions would TOLERATE each other, as their religion dictates. Turning the other cheek, letting people move along the wheel, honouring your guests. The remaining 2% would be fundamentalists and extremists, but such people have a shaky grasp on reality as it is.
Religion, race, caste.. they're not the reasons for war, but its the reason someone will give you, because these things are immutable, and thus "not their fault". God told me to, they're an inferior race, they're untouchables and pariahs. I'm just following orders.
Sadly, it will not change.