You have a point in 1 to an extent, but by this logic we can never compare the Islamic world and Christendom WRT anything.
I think it's more or less unquestionable that modern secular countries with Christian majorities are, on average, much more tolerant than any muslim country has ever been at any point over the last 1000 years, and you say that you don't contest this, but then, how are we to compare? It's not the degree of tolerance reached but the length during which one was slightly more tolerant than the other over the last 1000 years, or the total religious body counts? Are we just comparing "Christianity" and "Muslims", or are we to differentiate according to sects?
It seems like a difficult exercise. The people who suffered the most from ("religiously motivated") violence from christians are probably other christians, and it's probably the same thing for muslims. The huge time-frame makes comparisons difficult, as faiths and their interpretations hugely evolved not only through the centuries but from one place to another, and the huge concentrations of powers which took place in the different kingdoms over those centuries means the level of tolerance often had more to do with the personality of the leader than the religion, imo - there were "tolerant" leaders in the Christian and the Muslim world, and there were also intolerant ones in both. In both "spheres", religious movements survived or developed themselves thanks to local tolerant leaders, or at least not entirely genocidal ones, and in each, entire churches and religions disappeared due to extremely harsh intolerance. Plus, the rise of tolerance in most "christian" countries over the last centuries has also got a lot to do with factors which are external to Christianity.
It seems kind of pointless to compare, for instance, the Bangladesh genocide to the Thirty Years' War, and it becomes very difficult to know what should be counted as religious, or even as "tolerant", and what shouldn't.
There are also lots of events which are covered by few historical sources, making death counts and comparing relative tolerance difficult... For example, the way Christianity disappeared in Maghreb following the Muslim Conquests, or the way Timur treated Nestorians.
I think you're question is better suited for AskHistorians than CMV though, but, all in all, I think it's unanswerable in its present form.