Bartimaeus,

I would argue that you cannot generally hold the religions responsible for the killings that you mention. In most cases the religions themselves prohibit such killings and instead you have individuals who intentionally misrepresent the religions to further their own goals.

Case in point is the Spanish Inquisition. Certainly, the Catholic Church was involved since the monarchs who persecuted the Jews in Spain were Catholic, but those monarchs pressured the pope to allow it and then went far beyond the original charter. In general, an Inquisition would only apply to those baptized as Catholics and would result in fines or imprisonment if they were found to be heretics. The Spanish Inquisition, under direct control of the king, imposed torture (rarely) and the death sentence (even more rarely) on people who were not baptized Catholic, which was beyond what the pope had allowed, but the pope was unable to stop the Spanish monarchy in their actions. The monarchs were indeed the responsible people here and the religion became the scapegoat. Thus one cannot blame the Catholic religion for these killings, but instead the goals of King Ferdinand II of Spain (who was attempting to pull his country out of hundreds of years of Moorish rule).
As you suggest, religion is simply an excuse in this case, but if religion didn't exist, do you think that the exercise of power would not have happened? When Ferdinand came to power and began unifying Spain, he needed (in his view) to gather control under himself and that meant that he was going to use his power to put down dissidents. Even without religion there would have been dissidents and even without religion, Ferdinand would still have imprisoned and even killed people who disagreed with him, so while religion may be an excuse, it isn't a cause, and excuses are interchangeable, there would simply have been another one if religion weren't available.

Similarly, you'll find that most killings that are blamed on religion in fact should be attributed to individuals who have their own agendas.

That isn't to say that religions are totally blameless. There are some religions that encourage killings of those who don't follow their religion and there are some who have actively engaged in killings, but are they the majority?

You said that "the effect of religion all over the world ... has lead to many killings." I would argue instead that the major effect of religions all over the world has been to allow adherents to explore their spirituality and their faith and a small side effect has sometimes led to violence and death (as will any enterprise taken by human beings).

-- Jeff

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"Government is not the solution to our problem, government is the problem." --Ronald Reagan