What inquisition?

Apparently, the Catholic church downplayed to death count due to inquisition while they asked to be forgiven for it. http://after-words.org/grim/mtarchives/2004/06/Jun161425.shtml
According to skeptics, religious violence has led to many millions of murders, not just through Christians or inquisition, in the past millennium. http://www.theskepticalreview.com/JAHPoliticsDeathToll.html
How then am I to reconcile the church's apology, the fact of the killings, Christians' destruction of sacrificial "pagan" beliefs around the world, skeptics' accusations about religion as a source of violence, and the assertions of other Christians I know personally that none of them would support such actions? How then, also, am I to handle the remains of my pagan heritage, destroyed as it were by evangelism? Should I claim the Catholic supplanters' faith, the older beliefs, both, or neither? Which path would gain me the richness of an established tradition which will live on for generations after me? Sometimes we cannot learn answers, only questions. The rest is up to us. I sure wish I had a narrative to guide me, but the clearest story in the Bible is actually composed of four viewpoints, and the ancient narratives of my culture appear to be lost.
I guess I should love each person, as Jesus would do. Then, I should judge their actions as closely as I can to how God would. It comes down to credibility, after all. We shall know them by their fruit, not what they say or what they believe. A Satanist who harms no one is a good person. A Christian who engineers the destruction of others is evil. My beliefs do not change. Like a skeptic, I say that I have a higher standard of morality than Christians. Knowing skeptics, I believe I am more truthful than they.