The big difference is that it was never the policy of Christianity to do those things. These “atrocities” were usually politically motivated things, using religion as a pretext, and at times (including during the Spanish Inquisition, which the Pope tried numerous times to halt) even Church authorities could not prevent them.
One of the biggest mistakes in our understanding of Islam is to confuse the evil and in fact disobedient and non-Christian actions of a few supposed Christians with the officially established policies and laws of an entire religion, Islam, which is evil and violent not because of misinterpretation, but precisely because of its core beliefs and policies.
It is tragic and ridiculous that basically anti-Christian societies that persecuted, tortured and killed faithful Christians (for crimes like owning a Bible) are today portrayed as “Christian” in nature by the dominant media. There is this insanely ignorant mindset that all of Europe was always Christian for the past 2 millenia, so anything that has happened there was straight out of the Bible. In reality Christian influence, though profound, has been sadly more limited, and Christians usually a small minority of most of these cultures (secular ‘churchians’ being far more dominant.)
Isn't that the truth. One need only to look at the foundational documents of each--the Bible, especially the New Testament vs. Koran and Hadith. Jesus taught a spiritual kingdom "or else my disciples would fight" (John 18:36)) which would eventually have effects on the political/material world. Now of course after the Church got mixed up into the state--with Constantine than into the Middle Ages, things got messed up, but none-the-less, even then, Christianity spread by force was the exception, not the rule. The Koran though assumed a worldly kingdom...not a spiritual one...spread and maintained by force.
Mohamed though was a bandit-general--who got his will by force of arms. The Arab armies invasions started immediately after Mohamed died, and the first 4 Caliphs--successors to Mohamed--were all assassinated.
Quite a different history, and scripture, than Christianity.