Statements made on the cruelty of religions are factual; I would agree to that. The answers however flows over philosophy, religion, history. Have done my little best to explain this in a rather large nutshell. Religions have been instrumental in brutal elimination of precious human lives. We see that till today. With false ideologies, twisted scriptures, lying books that fuel hate, fuelling human desires for power and lust. Atheist authors like Christopher Hitchens, Michael Shermer, and Sam Harris are always debating religious authors like Dinesh D’Souza, William Dembski, William Lane Craig, John Lennox and Alister McGrath about whether or not God exists, or whether or not religion is good for the world. And, as predictably as the sun rises, these debates nearly always devolve into the argument of which side is responsible for the greatest death toll throughout history. Which is a more terrible killer: religious fundamentalism, or the lack of religion? In the background any killing from any ideology is certainly to be abhorred; be it from a Theistic perspective or from an Atheistic perspective.

Here there is no denial of the crimes in the name of religions.
Adding to your statement;
[a] from the early roman catholic church that burned people at stakes, fought and promoted wars
[b] to the very later mid-east ideologies that scream page after page of so called scripture that killing unbelievers gives heaven,
[c] the replacement theology doctrine where Jews was persecuted by protestant Christians,
[d] the recent religion based mass murders in our own India from godhra to Orissa
[e] now in Syria people kill each other crying out that god is great while slitting throats and bombing civilian
[f] middle east, televisions scream asking people to kill Jews for reaching heaven. This is a full blown shame no doubt.

All are poignant pointers to the wickedness and venom that can be injected into the populace in the guise of religion.

DOES RELIGION PROMOTES VIOLENCE?
Not all religions promote violence against humanity. Yes few religions directly do and even gives killings as a religious duty to the followers on killing anyone who do not believe in their tenants; and there are those few who absolutely don’t. There are the others although do not promote violence but still are used by men to pursue their own wicked objectives. Further down the spectrum there are also a few lines of thought that only promote peace and non violence and do not even believe in killing animals.

ARE NON VIOLENT RELIGIOUS IDEOLOGIES USED TO PROMOTE VIOLENCE?
Even non violent ideologies sometimes generate passions that are harnessed for evil purposes by a few in their quest for power and dominion. Yes, hundreds of examples.

DOES THIS MEAN THAT ATHEISM IS THE MORAL FORTRESS?
But this does not give Atheism a moral ground to stand and mock any organized religion since the data shows there are more lives lost and plundered by atheist regimes across than people killing inspired by religion. This is no different from organized religion inspired crimes. Where is the moral ground? The influential deist philosopher Voltaire, criticized established religion to a wide audience, but conceded a fear of the disappearance of the idea of God: “After the French Revolution and its outbursts of atheism, Voltaire was widely condemned as one of the causes”, wrote Geoffrey Blainey, “Nonetheless, his writings did concede that fear of God was an essential policeman in a disorderly world: ‘If God did not exist, it would be necessary to invent him’, wrote Voltaire”

Vox Day notes concerning atheism and mass murder: “Apparently it was just an amazing coincidence that every Communist of historical note publicly declared his atheism … .there have been twenty-eight countries in world history that can be confirmed to have been ruled by regimes with avowed atheists at the helm … These twenty-eight historical regimes have been ruled by eighty-nine atheists, of whom more than half have engaged in democidal 162 acts of the sort committed by Stalin and Mao … The total body count for the ninety years between 1917 and 2007 is approximately 148 million dead at the bloody hands of fifty-two atheists, three times more than all the human beings killed by war, civil war, and individual crime in the entire twentieth century combined.

Atheism hence has no moral ground as its a bigger perpetrator of crimes against humanity than all the religions put together and all the wars put together in the 20th century.

I would personally invite you to pursue the following counters from a Christian perspective.

http://www.wnd.com/2013/03/horrific-human-toll-of-militant-atheism-exposed/

http://www.str.org/articles/the-real-murderers-atheism-or-christianity

http://www.conservapedia.com/Atheism_and_Mass_Murder

http://www.csmonitor.com/2006/1121/p09s01-coop.html

Media:
Atheist Killers – The Lie that Religion leads to Violence https://www.youtube.com/watch?v=GRxgBG-YnPQ
The Moral Foundation Dr Ravi Zacharias: https://www.youtube.com/watch?v=u6rg6f5Y5CI
A Debate by Christian Apologist vs Atheist: https://www.youtube.com/watch?v=3vnjNbe5lyE
Another Debate: https://www.youtube.com/watch?v=XcnZRctcleM
Dawkins Tells Atheists To “Mock Religion With Contempt, and a Christian response: https://www.youtube.com/watch?v=51rR4aC9aMg

WHICH WORLD VIEW REINS AND REIGNS IN MORALS? ABSOLUTE MORALITY.
Now on morality; Religion does preach morality; from a Christian perspective yes and we know the levels of holiness, purity expected from us. But when it comes to the term “Morality” it exists only in the premises when God as an overseer exists. If we believe in the naturalistic and materialistic perspectives of this world and that matter is all that is; then debates can be set that morality is not in any way a requirement that too in the wake of evolutionary dogma where we being evolved chimps should not even term killings a crime. We an evolved higher animal should allow all acts of necrophilia, pedophilia, rape, loot, cannibalism, homosexuality and further incorporate all that can subscribe to the Darwinian thought of ‘Survival of the Fittest”. Pol Pot’s, Stalin’s dogma then is a true adaptation of such an idea. Even Hitler in his Mein Kampf speaks about the Aryan race and the survival of the fittest. Atheism is fully bankrupt in terms of morality; the prime evangelists of atheism fully know that there is no eternal and transcendent standard for right and wrong by adopting moral standards on the pillars of atheism. The Nazi movement, based upon an evolutionary eugenic ideal of developing a super race, destroyed those deemed by them inferior or unsuitable. Many atheists who are judgmental of religious people who have committed great atrocities, but upon what basis? Does this make any sense? Atheistic assumptions irresistibly lead to the conclusion that morality is nothing more than a matter of personal or societal preference. If humanity is left to create its own ethical standards, we are left with only few options to base ethics upon: 1) collective tradition, 2) human survival, or 3) personal preference.

The best; William Lane Craig – Where do Objective Morals Originate: https://www.youtube.com/watch?v=Rmg720wO6tY
Atheism and the Answer to Slavery, Child Abuse, Genocide… https://www.youtube.com/watch?v=kvhGsEsVda4
The Moral argument for God; How Can We Demonstrate that Objective Moral Values Exist: https://www.youtube.com/watch?v=fbeoe2_6qx4
The Moral Argument for God; There Is A Difference Between Absolute and Objective Moral Values: https://www.youtube.com/watch?v=cUE4cwNuSZ4
Is Atheistic Moral Platonism More Plausible Than Theism? https://www.youtube.com/watch?v=VGWAVRoLQ3c
Why would God allow Evil and Suffering? https://www.youtube.com/watch?v=ixP7AAOMbgc

A CHRISTIAN RESPONSE TO THIS TOPIC.
In a religion such as Christianity [for which I can speak with my limited understanding] the preachings of Jesus Christ and the exhortations by the apostles, prophets heavily weigh down on any follower that killing is a crime. First Christianity as from Jesus Christ demands that we NEVER hate anyone.

The list of verses in the Bible in ESV [I would prefer KJV] that point to “Do not HATE”

Starting with the fact that Jesus gives that as a commandment. John 13:34-35 ESV > A new commandment I give to you, that you love one another: just as I have loved you, you also are to love one another. By this all people will know that you are my disciples, if you have love for one another.”

>1 John 4:20 ESV If anyone says, “I love God,” and hates his brother, he is a liar; for he who does not love his brother whom he has seen cannot love God whom he has not seen.
>1 Corinthians 13:4-7 ESV Love is patient and kind; love does not envy or boast; it is not arrogant or rude. It does not insist on its own way; it is not irritable or resentful; it does not rejoice at wrongdoing, but rejoices with the truth. Love bears all things, believes all things, hopes all things, endures all things.
>1 John 3:5 ESV Everyone who hates his brother is a murderer, and you know that no murderer has eternal life abiding in him.
> Proverbs 10:12 ESV Hatred stirs up strife, but love covers all offenses.
> Proverbs 6:16-19 ESV There are six things that the Lord hates, seven that are an abomination to him: haughty eyes, a lying tongue, and hands that shed innocent blood, a heart that devises wicked plans, feet that make haste to run to evil, a false witness who breathes out lies, and one who sows discord among brothers.
> Matthew 5:21 ESV “You have heard that it was said to those of old, ‘You shall not murder; and whoever murders will be liable to judgment.’
> 1 John 2:9 ESV Whoever says he is in the light and hates his brother is still in darkness.
> Ephesians 4:29 ESV Let no corrupting talk come out of your mouths, but only such as is good for building up, as fits the occasion, that it may give grace to those who hear. [according to this verse you may not even verbally show anger nor generate strife]

Further…
> Proverbs 8:13 ESV The fear of the Lord is hatred of evil. Pride and arrogance and the way of evil and perverted speech I hate.
> Romans 6:23 ESV For the wages of sin is death, but the free gift of God is eternal life in Christ Jesus our Lord.
> Ephesians 2:8-9 ESV For by grace you have been saved through faith. And this is not your own doing; it is the gift of God, not a result of works, so that no one may boast.
> Matthew 7:1-29 ESV “Judge not, that you be not judged. For with the judgment you pronounce you will be judged, and with the measure you use it will be measured to you. Why do you see the speck that is in your brother’s eye, but do not notice the log that is in your own eye? Or how can you say to your brother, ‘Let me take the speck out of your eye,’ when there is the log in your own eye? You hypocrite, first take the log out of your own eye, and then you will see clearly to take the speck out of your brother’s eye.

Still…
Luke 6:27-36 – But I say unto you which hear, Love your enemies, do good to them which hate you,
Luke 10:27 – And he answering said, Thou shalt love the Lord thy God with all thy heart, and with all thy soul, and with all thy strength, and with all thy mind; and thy neighbor as thyself.
Matthew 5:44 – But I say unto you, Love your enemies, bless them that curse you, do good to them that hate you, and pray for them which despitefully use you, and persecute you;
Proverbs 10:18 – He that hideth hatred [with] lying lips, and he that uttereth a slander, [is] a fool.

Christians who get involved in killing are not inspired by Jesus Christ to murder, massacre, these are deviant ideologies that stem from the rot in human minds. The instruction received is clear and absolute. No killing, no hate, not even a hateful word. If I speak a hateful word that does not mean Christianity professes hatred; its my human nature where I have not yet applied the morality that is demanded of me from Christ.

Christianity as a Religion does not cause you to kill people, and it certainly also does its best to prevent you from killing people. The same can be said for many world views except a very few where fanaticism rules the roost. I would love to debate on this anytime but we ought to reason as we may have found and unfound many logical and illogical points that might split the fabric of reason and land in a debate. We can choose to reason further.