Your conception of history is not so accurate. For example, the Crusades occurred after the Islamic expansion into Europe. Had the Muslims not been defeated in Italy during the 10th century you and I would be reciting the Koran every day. The Crusaders would probably not have occurred had Islamic nations not tried to move into Europe.
The Inquisition no doubt was a matter of religious intolerance. However, the numbers do not nearly compare to Stalin's oppression, or Mao's repression, or Cambodia's killing fields (all atheist governments by the way).
If you look at the 20th century, you will find of the people who were killed in the name of a cause (e.g., because they were terrorists, or because they were imperialist, etc) very few of those people (percentage wise) were killed in the name of Christ. In fact, how far back would one have to go before that is the case? And, even more so, how long and how widespread did the killing take place compared to the history and geography of the religion. These factors are usually not considered when the Inquisition comes up (btw, by that time the Catholic Church was a highly secular organization and one can argue that many of these persecutions were for political not strictly religious reasons). In any case, as a whole Christianity has been somewhat peaceful compared to the ugliness that humanity has seen from more intolerant religions as well more intolerant ideologies.
As for science, since the Christian society is the main society from which modern science emerged from earth, and most of those scientists were Christian (Newton, Kepler, Galileo, Leibniz, etc), I think it is fair to say that Christianity was conducive to the development of science. Yes, Galileo was put under house arrest, but he was not tortured and for the most part he was allowed to recant his support of the Copernicus. Yes, that was very horrible that even this event occurred, but it did not stop science. A short time later and the Copernicus doctrine moved forward. Of course, one could mention certain Soviet scientists who were put in the Gulag. A fair bit more unpleasant than Galileo's house.
Warm regards, Harv