Richard Dawkins, one of the most recognizable atheists in the world, has recently stated “mild pedophilia” does not cause lasting harm (http://www.salon.com/2013/09/10/richard_dawkins_defends_mild_pedophilia_says_it_does_not_cause_lasting_harm/). This is not a new idea from Dawkins, he previously state that he felt that the Roman Catholic Church pedophilia scandals were blown out of proportion and stated it to be so, in his best-known work, The God Delusion.
As many Christians are already aware, there have been a number of issues within conservative Protestantism involving sexual abuse as well. Most recently, in the secular media, Bob Jones University is being questioned about its counseling policies involving sexual abuse, including the question of required reporting, and while the report from their ombudsman is not in, a number of allegations have been featured in the press. Sadly, there are a number of voices that have argued that this is somehow an issue that is intrinsic to Christianity, Fundamentalism or Protestant theology.
Yet, Dawkins’ statements remind me of an earlier series, which I addressed on our more technical site: a series entitled “The moral argument from atrocities” (http://apologiafides.wordpress.com/category/moral-argument-from-atrocities/), where I compared monstrous acts committed by atheists and by Christians (or alleged Christians) to as the question of were those who committed atrocities logically consistent with their beliefs. I would like to make the same comparison between atheists who commit sexual abuse and those who claim to be Christians committing similar actions. While Dawkins is not being accused of Sexual abuse at this time, his statements are analogous in a sense to the current scandals faced by some Christian counselors.
As noted before, if their professions are genuine, Christians who commit sexual assaults are inconsistent monsters. (https://truthinthetrenches.org/2014/03/04/do-sexual-assaults-by-professed-christians-invalidate-christianity/). That is, their monstrous acts are not consistent with their professions of faith (in short, they are hypocrites); the same would be true for those who fail to report sexual abuse (Romans 12). Sadly, this cannot be said for atheists who commit these kinds of atrocities, or the lack of wisdom in Dawkins words. While it would be a logical fallacy to say that atheism leads to sexual abuse (just as it is when people argue that Christianity leads to sexual abuse), it cannot be suggested that atheists are hypocrites on this point. If there is no ultimate morality, if morality is simply a system established by society to preserve the group, then no sin has been committed.
So, if we compare the questions surrounding Bob Jones University with the statements made by Richard Dawkins, then, if the allegations are ultimately proven to be true, Bob Jones, sadly, has not lived up to the beliefs, which they espouse. Richard Dawkins, however, is living up to his.
Truth in the Trenches 
You’re right. Atheists can’t be said to be hypocrites for sexual abuse. Theists can’t either. They can be called hypocrites for preaching one way and acting another, or by saying that theism leads to morality and atheism leads to immorality. If theists can do bad things, then clearly that isn’t the case.
However, Dawkins is a hypocrite. He’s a hypocrite for becoming a social justice warrior and fighting for equality for atheists, and then turning around and mocking people for being social justice warriors. People who sexually assult people aren’t necessarily hypocrites, though they may be, they are worse than that: they are criminals who view others as objects for their own desires.
Actually you have a couple of errors in this, because you don’t understand the Christian religion. Christians believe that mankind is already evil – the problems of our society begin in the depravity of the human heart. While mankind has a conscience, and is capable of some good outward actions, it is not our natural bent. Christians who practice sexual abuse are hypocrites because they are not practicing a Christian moral code; and that assumes that the claims of being a believer are genuine.
Also Christians do not so much say atheism will lead to immorality, we believe man is already immoral to begin with. Our argument is that Atheism is a step down in the decline of societies (described in Romans 1), it is both a result of immorality and removes barriers towards society declining faster. In a sense, Atheism is a step in God turning people over to the depravity of their own mind, of His giving up on people.
You stated “If theists can do bad things, then clearly this isn’t the case.” The central problem with your point is that few Christians believe that Christ leads us to sinless perfection, and Paul regularly reminds us of the dangers of “the old man.” We argue that moral improvement is the general trend, but not a universal principle where the switch is flipped and suddenly we become perfect, we wish it was so easy. Paul talks in Romans 7 for example about his own struggle with sin, probably covetousness.
You are also assuming that outward profession of faith (ie someone saying they are a Christian) or intellectually accepting the doctrinal beliefs of Christians, and must have benefited from Christianity. The problem is that the faith doesn’t teach this either, we are warned throughout the New Testament that there are tares among the wheat, smuggled in false brethren, and other similar terms to describe those who claim to be Christians, but have not experienced regeneration. I realize that as an atheist this is not something you would accept, but it still means your argument is a strawman, because it doesn’t accurately describe what Christians actually believe.