The Crusaders of the first crusade spent the day after taking the cross murdering Jews. Meanwhile Moses Maimonides, the greatest Jewish medieval scholar, was a respected figure at court in Egypt and Syria. When Moorish Spain was reconquered by Christians, many of the Jews fled to Turkey or Holland to avoid the persecution that immediately followed. Some of those that went to Holland remembered what religious tolerance had been like, and not long afterward the Dutch revolt from Spain was the first successful Protestant revolt from a Catholic king. Tolerance had to be relearned in the west, and medieval Islam had a small part in that process.
And they did listen to reason in theology at one time. Alfarabi, Avicenna, and Averroes were not committed to darkness and persecution of free thought. They even influenced western theology, particularly that of Acquinas. Some of their own theologians opposed these tendencies, out of fear of secularism. They threw the baby of reason out with the bathwater of unbelief, and the Islamic world has produced precious little in the way of science or learning since. Some thinkers in the Muslim world in our own day have recalled this, and suggested it was the key mistake. Avicenna could have been their Acquinas, if they had listened. It is not too late for them to start listening now.
I understand your religious outlook on history, but it seems to me it leaves too little room for the known nuances of wickedness. If Christianity taught that all Christians are righteous, your reading, true or false, might be the Christian one. But that is not Christian doctrine. Christianity does not insist on the universal righteousness of Christians, but on the universal fallenness of all men. All men can be evil. Many outwardly profess what they in no way understand in their hearts. Many crimes caused by human passions - greed and hatred, ungoverned zeal, love of power - have been dressed in pretty language. This makes it untrustworthy to judge men and deeds by outward professions of religious affiliation.
As Lord Acton put it, "in judging men and things, ethics go before dogma, politics, or nationality. The ethics of history cannot be denominational. Judge not according to the orthodox standard of a system, religious, philosophical, political, but according as things promote or fail to promote the delicacy, integrity, and authority of conscience. Put conscience above both system and success.
"The moral code is not new, it has long been known. It is not universally accepted even in Europe, even now. The difference in moral insight between past and present is not very large. But the notion and analysis of conscience is scarcely older than 1700, and the notion and analysis of veracity in history is scarcely older than our own time. In Christendom, time and place do not excuse - if the Apostle's Code sufficed for salvation. A good cause proves less in a man's favor than a bad cause against him.
"Faith must be sincere. When defended by sin it is not sincere; theologically, it is not faith. God's grace does not operate by sin. Transpose the nominative and the accusative and see how things look then (i.e. apply the golden rule). The systems of Barrow, Baxter, Bossuet are higher, spiritually, constructively, scientifically, than Penn's (Quakers). In our scales his (Penn's) high morality outweighs them."
In addition to Acton's wise words on the subject, I point out the effect that religious tolerance in the Muslim world would have for your own religious outlook. Missionaries can operate wherever there is tolerance, but cannot breath where it is not recognized. Islamic orthodoxy today regards apostacy from Islam as not only a sin, but as a capital crime. There is little prospect of evangelizing the Muslim world before they learn the principle of freedom of conscience.
Religious confidence ought not to shrink from freedom of conscience. To confess a dependence on intolerance, or on fighting another religion as an implacable enemy with physical rather than spiritual arms, is to confess a lack of faith in the attraction of truth. It is in the interest of your religious views too, no less than in the interest of justice among Muslims, and in our country's interest in its relations with Muslim countries, to see religious tolerance established in that part of the world.
Nor are you "allowed", theologically, to give up on one sixth of the human race. Justice may arise where it is least looked for, even in a despised malefactor at the gallows - when no one else understood - if only he is willing to say rightly "but this man has done nothing wrong." Charity, Chesterton once said, is a mystical agnosticism about the complexities of the soul. For what it is worth.