Let me be clear: I am not sanctioning the internal persecution of Christians on sectarian lines. What I am saying is the systematic genocide of Christians under various Islamic regimes, especially those perpetrated by Tamerlane* and the Ottoman Empire*, and most recently under the Islamic State**, and under militant atheist regimes like the Soviet Union, especially in its early years (the persecution mellowed out during the WWII era), in Albania under Enver Hoxha, in Romania under Ceausescu and his dreaded Securitate, and in North Korea, was infinitely worse. Indeed, these genocides can really only be compared with the Holocaust in terms of scale and comprehensiveness.
Also the one million figure you cite on witches strikes me as being high; I will have to look into it; there is no denying however that there has been a horrible amount of violence between supposed Christians, and genocides, for example, the Crusaders who killed large numbers of Eastern and Oriental Orthodox Christians and did in some instances cannibalize them, before the Fourth or False Crusade, an event which so weakened the Byzantine Empire, that its collapse 243 years later became an inevitability. However, it is ultimately besides the point; my point is that militant atheists do have actual blood on their hands and a massive amount of it, as well. Communist atheist dictators I would argue have been the second worst external persecutors of Christians, after radical Muslims (primarily radical Sunni Muslims like Tamerlane or the Young Turks*** who seized power in the Ottoman Empire in 1909). The Roman persecutions, which only temporarily stopped under Constantine, before continuing into the reign of Theodosius, easily come in at no. 3.
