"Science flies you to the moon, religion flies you into buildings."
It's ironic that one of the most common disputes atheists walk into against "religion" also happens to be the hardest for them to win. They love to claim not only the intellectual high ground, but even the moral high ground. It may be that they attack "religion" as a whole. It may be that they attack Christianity for something some Christian or group has done in the last 2,000 years (or, more likely, within the last 1,000). It's especially common for them to cherry pick a few Bible verses and make the Bible seem as scary as possible.
All of these fail on a number of levels. To begin with, "religion" is too broad a term. In fact, the only worthwhile definition of "religion", that being "a belief about the cause, nature, and purpose of the universe", also covers atheistic religions, such as Buddhism, Taoism, and Evolution. Because religion is such a broad term, it is actually illogical to dismiss it all with the same argument. Each religion should stand or fall on its own merits, not being held accountable for the flaws or crimes of other religions. In fact, it seems to me the main reason atheists so desperately cling to this broad term is precisely because Christianity does stand on its own merits, and is virtually impossible to adequately criticise when taken on its own.
But the atheist might suggest Christianity actually falls regardless, since it is allegedly a violent and evil religion. The low hanging fruit here would be to point out that atheists have also committed many great atrocities, and far more recently than any Christian group. Many great horrors have taken place in the name of atheism, or have at the very least been justified by atheism. But the real question is, can they be justified within atheism?
To be 100% clear, in and of itself, atheism does not prescribe anything evil. In fact, it completely erases any and all foundations for morality. Therefore, it doesn't prescribe anything at all. Not even empathy. What that means is whenever an atheist says something like "if you need a god to tell you not to rape, you don't lack religion, you lack empathy", they must borrow from a Theistic religion in order to justify empathy in the first place. In atheism, there is no reason to assume one "should" do, or not do, anything in any given scenario.
As a Christian, I have a clear and defined source of morality by which I can reasonably judge human behavior. I can not only say "this is good" and "this is evil", but even "this is/is not consistent with the Christian faith."
To give an example of an acceptable thing, let's take the consumption of alcohol. Biblically speaking, alcohol is a neutral thing. Although there are limits, alcohol itself is a blessing God has given man. Thus, the answer to "can a Christian drink alcohol?" is a complex one. It's a "yes, if", rather than a firm "yes" or "no".
An example of a good thing is charity. Although Christians are never supposed to give under compulsion, or begrudgingly, thereby eliminating abusive practices such as compelled tithing, it is quite clear that God is pleased when we give generously and cheerfully, and is even more pleased with us when we do so from a position of lack.
An example of an evil thing is abortion. Scripture makes it very clear that human beings are made in the image of God, and the termination of our lives is not a thing to be taken lightly. He will occasionally delegate the authority to kill to another human being, or more likely body thereof, but this is exceptionally rare. As a baby is a human life long before its mother even knows she is pregnant, it is murder to kill them in virtually every circumstance, with the sole possible exception being if carrying the pregnancy to term is life threatening, in which case the argument can be made that the situation has become a matter of self defence.
So, here we have 3 examples of moral choices. Alcohol is a grey area; it can be justified, but with limits. Charity is a green area. It is an objectively good thing, and it is suspicious if a Christian is hesitant towards it. Abortion is a red area. It cannot be justified, with very few exceptions, if any.
But when it comes to atheism, all of these are grey areas. You can drink what you want, do good to whoever you want, and kill whoever you want. In atheism, the one who is "right" is the one with the biggest gun. Even then, they're not necessarily right, they just happen to have the power to enforce their will on others.
Because of this, every time an atheist makes a moral claim against any religion, they must actually borrow from religious principles. That is, they are saying religion is bad by affirming the goodness of religion. Furthermore, by affirming that there is a moral standard, they are necessarily denying atheism by exposing its moral bankruptcy.
This is where the Bible ends up reading atheists like a book. In Romans 2:12-16, we read "For as many as have sinned without law will also perish without law, and as many as have sinned in the law will be judged by the law (for not the hearers of the law are just in the sight of God, but the doers of the law will be justified; for when Gentiles, who do not have the law, by nature do the things in the law, these, although not having the law, are a law to themselves, who show the work of the law written in their hearts, their conscience also bearing witness, and between themselves their thoughts accusing or else excusing them) in the day when God will judge the secrets of men by Jesus Christ, according to my gospel."
This, ironically, affirms an atheist talking point in a way atheists would prefer it not be affirmed. You genuinely do not need to know God to know right from wrong. See, just as God teaches chicks how to break out of their eggs, He has laid certain moral instincts in the hearts of all men. Thus, we all naturally follow His laws to an extent. The problem is, we also break them far more easily, and in fact prefer to do so. When atheists object to God's alleged "evil" in the Bible, they're always looking at how He deals with sinners. Thus, they object not because He is genuinely evil, but because they are.
But there is good news in that God's goodness extends beyond wrath against sin. In His love, God takes no pleasure in the death of the wicked, and so instead, He sent His Son, Jesus, to live a perfect life as a man. In spite of His perfection, Jesus died the death of a sinner, receiving the full wrath of God for sin. This allows us to effectively "swap verdicts", with the one and only condition being faith. All who confess Jesus as Lord and believe in their hearts God raised Him from the dead will be forgiven for every evil thought, word, and deed, receiving eternal life from the same.