That would be the period between 305 and 1945.
Anti-pagan legislation only started to appear in the 350s (under Constans and Constantius II), and it wasn't enforced until the 390s (under Theodosius I). Even then it was nothing like on the scale of the anti-Christian legislation of the pagan period. Remember that the Christians did not start actually executing people for paganism until the time of Justinian - two centuries after Constantine. The pagans, by contrast, had started executing Christians about thirty years after the religion first appeared.
They'd want to, but my count grants the highest carnage due to religious intolerance at the hands of the Christians. To me, it centers around the glorification of "faith" -- of accepting what you are told on faith and without question. Religious power and authority are at least as easily abusable as military, political or economic power thanks to the unquestioning hold it has over so many.
Those who question why the town of Salem, Massachusetts rose up for a horrendous act straight out of the dark ages, burning girls to death based on "he said/she said" rumor and superstition without questioning their rationality, or why the Christian majority in Germany supported Hitler's rise to power without too many qualms, as well as how pedophilic priests get away with their horrible sins for so many years, I think fail to understand this. It doesn't even matter whether or not there is a God -- from sheer peer pressure, you go along with where the flock is going, even if the shepherd is leading the flock to the slaughterhouse.
I don't disagree with your assessment of religious authority as being as abusable as other forms of authority. However, don't think that the Salem incident would have been more appropriate to the Dark Ages. The major periods of persecutions of "witches" were in antiquity (Livy describes some major purges) and the early modern period. The Middle Ages, including the "Dark Ages", were one of the least witch-hunting periods of history. This was, in large part, because the Catholic Church at that time denied that witches existed and discouraged such activities. In fact we're currently living in a time of increased "witch" hunts, if you consider what's going on in a number of African countries with regard to so-called "witches", including many children.
The question whether Christians have caused more deaths through religious intolerance than they have suffered is an interesting one. There's no way that we can collate accurate figures for either group, but let's have a go to see if we can get an approximate guess by looking at the most significant events that we'd need to consider.
I'll leave out the numbers of Christians killed by other Christians, since they would presumably be added to both columns anyway and therefore not affect the result.
People killed by Christians
This is people killed by Christians specifically for religious reasons, rather than people killed by Christians who happened to be of another religion. So I won't count, for example, the actions of the conquistadors.
First, pagans persecuted in late antiquity and the early Middle Ages, under the Byzantines and the emerging Christian powers in Europe.
Very hard to estimate figures for these, but I think they must be small. In the Byzantine empire, there were very few pagans by Justinian's time, although certainly there were some. Their earlier resistance had been broken in the 390s by a series of legislation and the battle of the River Frigidus. As far as I can tell, most pagans were forcibly baptised or were suppressed in similar fashion, rather than being executed, although certainly some were. Manichaeans were also executed. So I don't know what kinds of figures we're talking about here, but my guess is that it's in the hundreds. As for western Europe during the first millennium AD, it is even harder to guess, except that as far as I can tell execution was again not a major feature of the process. Certainly a lot of pagans got killed in the process, but then so did a lot of Christians too. Once again it was more a matter of suppressing pagan practices rather than killing pagans. If we count events such as Charlemagne's killing of pagan Saxons in the course of his wars against them, then we've got perhaps a few thousand deaths.
Then we have the northern crusades, as they are sometimes called, conducted by the Christian Scandinavian powers against their non-Christian neighbours. Whether we can really count
wars of this kind as "religious persecution" is a moot point, but let's assume that we can. A problem is that I have no idea how many people died in these wars.
The Albigensian crusade, a more obvious example of massacres fuelled by religious intolerance. Certainly tens of thousands of people killed here.
The inquisition - shouldn't really be here as it's Christian-on-Christian persecution, but still. Probably around 2,000 deaths in total.
The witch hunts - again, shouldn't really be here, for the same reason. The notion that the "witches" were practitioners of ancient pagan religions is a modern romantic myth; in fact they were just ordinary people. Estimates of the dead vary wildly but a figure of around 35,000 is now considered most probable. (Ronald Hutton, the major authority on this subject, gives a figure of double this.)
Persecutions of Jews throughout the Middle Ages and early modern times. (I'm talking about
religious persecution rather than modern, racially-based persecution such as that of the Nazis.) Again the numbers here are impossible to estimate but certainly very large, given the massacres that occurred during various of the Crusades. I'm going to make a wild guess of 100,000 people, but perhaps this is a severe under-estimate.
Killings of Christians
First, the afore-discussed Roman persecutions. A couple of thousand deaths, perhaps.
Next, the Sassanid persecutions. Far more wide-ranging - certainly tens of thousands of deaths.
Massacres during the Muslim invasions of the seventh century - for example, the mass killings of Coptic monks during the invasion of Egypt. I have no idea how many people these would be, but let's say a few hundred.
Tamerlane's campaigns - enormous numbers of Christians killed, making Tamerlane, I suspect, the greatest single persecutor of Christianity in history. His campaigns were what basically destroyed the Church of the East, at one time larger than the Catholic and Orthodox churches put together. Christians massacred, evicted, or forcibly converted throughout central Asia, the Middle East, and Armenia and Georgia. Certainly tens of thousands of people killed, probably a lot more.
Now the modern period:
Vietnam: Vietnam was divided into two kingdoms during this time, and this gave both regimes an added reason to be suspicious of Christians, whom they both suspected of being spies of the other kingdom. Around 30,000 Christians are thought to have been killed there during the seventeenth and eighteenth centuries. This situation continued into the nineteenth century: just between 1857 and 1862, 5,000 Christians there are thought to have been tortured to death. This situation ended only with French occupation in the later nineteenth century. So there were certainly many tens of thousands of Christians killed here throughout the period.
Japan: by 1600 there were some 300,000 Japanese Christians - the Catholic missions there had been exceptionally successful. Toyotomi Hideyoshi and Tokugawa Iyeyasu ordered a number of attacks on Christians but they were not effective. Tokugawa Hidetada and Tokugawa Iyemitsu conducted far more thorough persecutions. Certainly thousands of people were killed, thousands more were tortured. The church was effectively destroyed completely, leaving only the Kakure Kirihorsehockyan, who slowly forgot their faith over the next two and a half centuries.
Korea: the church here grew quickly during the nineteenth century and was stamped upon by the authorities almost as quickly. Priests were routinely tortured to death and there were many massacres. The worst were in the late 1860s, when around 10,000 Christians are thought to have been killed, and many more died of starvation.
China: there were periodic persecutions during the eighteenth century, the greatest being in the 1780s. But I don't know what the numbers would be. The Boxer rebellion in 1900 saw tens of thousands of Chinese Christians of all denominations killed: Christians were among the Boxers' chief targets, as representatives of foreign religion. The Cultural Revolution saw many Christians among its victims, but I don't know how many.
Communist Europe: certainly many Christians died in Stalin's purges, but I don't know roughly how many. Other communist countries suppressed the churches but didn't tend to kill people quite so much.
These are just the major persecutions by and of Christians that I can think of off the top of my head. There are certainly many others in both categories, but I suspect more in the latter than in the former. I haven't touched on things like the Armenian genocide where it's less obviously a case of
religious persecution. It seems to me pretty clear from these figures that the persecutions
of Christians are almost certainly much greater than those
by Christians, overall, but again, this can only be a guess of the roughest kind, not least because it is not easy to establish which events count as religious persecution in the first place.
