They didn't erase them because they needed a slave populace. They needed someone to feed their Janissary machines and to be the ones the outlaws and the law both picked on. IE. the Copts in Egypt. Mubarak prosecuted them, the Muslim brotherhood persecuted them, both sides treated them as Dhimmis-second-class citizens, according to their religious rites, and Muslims did that for centuries. When both the law-abiding Muslims and the bandit outlaw Muslims attack the Copts, and nobody from the Muslim community did anything about it, then it is Islam since nobody from the Muslims dare lifted a finger, and if one did, he or she is persecuted for standing up for the Dhimmis. Even when the Spanish Inquisition persecuted the Muslims and Jews of its day, they at least ALLOWED the Jews and Muslims to leave first, and even in those days, the pope himself condemned the Inquisition, which was hijacked by the Spanish monarchy, and he showed his displeasure by opening the gates of Rome to refugees escaping the Inquisition. But for the Orthodox Christians in Greece during the days of the Ottomans, the Armenians and the Copts and even the Iraqi Catholics who suffer today from persecutions and kidnappings, there were no Muslims who stood up for them. Not amongst the Muslims, anyhow. The problem is that the "enlightened" Muslims do nothing while the backwards hicks Muslims are the ones who are allowed to do whatever they want. Apathy is a sin of omission. A sin of doing nothing while people whom they could easily save suffer. Apathy is death. It is worse than death, since at the very least, the dead feed the maggots and the crows.
Even during the earliest days of the Crusades and the Inquisition, to the days of its height of power during the Renaissance, there were people in Christendom who fought against them. Roger Bacon, an influential Franciscan and the inventor of the Modern scientific theory, condemned the Crusades saying that the victims will just be hardened against the Cross. During the Inquisition, local bishops and their lackeys protested and resisted this papal or monarchial intrusion in a matter that they themselves should handle; the reason why Inquisitor Heinrich Kramer wrote the guide to hunting witches and tried to institutionalize witch-hunts was because of the fact that he was pissed off that the local churches thwarted his witch-hunting attempts and sided with the defendants whom he accused of witchcraft, and even later, his fellow Inquisitors threw away the book and it was used later on, ironically, by the enemies of the Inquisition such as the Protestants when "hunting witches" - an activity the Renaissance and Reformation Inquisition vehemently opposed.
If Medieval Christians (and Muslims) can outdo modern Muslims in standing up for minorities, then something is wrong.