Pretty shoddy gods who create us as beings capable of committing crimes even if we believe in them and their eternal punishments.

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The conundrum of Parenting in a nutshell!  

Free Will is the standard answer to that.  God does not want automata.  One is given the opportunity to chose or deny.  To deny is the choice to "go your own way" and not serve/obey.

Prisons around the world are full of both good and bad people.  That's for sure.  The Justice System is most certainly man-made.

Communists were explicitly atheistic.  Social dogma can easily replace religious dogma and lead to equally great crimes.  One might even argue the Crusades were more politically motivated than religious---but to be truthful, I'm not terribly informed about them.

Without a doubt, Mankind is quite good at manipulating each other.  Finding truth on a personal level is quite a struggle.

Where was the moral compass of religion to say slavery was wrong through those many wicked years of the Atlantic slave trade.

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The Abolitionists.  The North.  The Civil War.

The South was non-religious?

Why did the United States embrace abolition so much later than Europe? Was it less religious?

Do you have a source that more prison inmates are religious than non religious?  Do they claim god told them to do their crimes? If so, what is the specific religious  breakdown?

I dont know where to begin with the claim that no crime was done in the name of atheism.  Beyond stated atheistic doctrines and regimes (past and present) that have clearly not done the "right things" there are I imagine a lot of low lives who commit crimes because they only believe in their immediate self interest and have no faith whatsoever.

If Hell exists there can be no free will. 

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Because of the implied punishment for non-compliance?

I would think non-belief in God automatically negates belief in Hell.  So no gun-to-the-head, really.

The South was non-religious?

Why did the United States embrace abolition so much later than Europe? Was it less religious?

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I think you might be conflating institutions with morality/faith.  I can't say anything meaningful about how people during those times were influenced by their churches, and/or what state of secularism and corruption existed in those institutions.  

Truly, it's in the institutions build by men that weld power where we seem to habitually get it wrong.  Even in the New Testament, it's the religious leaders of the day who were pushing for the crucifixion.  Power almost always corrupts.  (...and logic is a slave to desire.)

To your other point: how often are minds changed and anything settled by debate and discourse?  ...even on the internet?

When I was a young man, I thought people could easily change.  Just explain to them why they are wrong...etc.

That belief was quickly crushed and I began to suspect people NEVER change.

I finally arrived at the notion that people do change.  It just takes enormous pressure from all sides---like making a diamond out of coal.

Abolition is actually a great example of how minds are changed by debate and discourse. The vast majority of countries managed to implement it without going to war -- the abolitionists simply appealed to the better judgment of the lawmakers. Public opinion may not change quickly, but it can change. Often with campaigns, appeals, and a good deal of tenacity. 

The religious texts always say the same thing. The consensus view on homosexuality, slavery, race, imperialism, animal testing, and so, changes, suggesting that the religious texts are not the guiding light that we rely on to make these decisions.

Even within the churches themselves moral views change, when their own most-valued texts do not. The Christian bible has said the same things about slavery and war and punishments for well over a thousand years. The majority Christian stance on many moral issues has massively changed over that time.

That a consensus view can change can be both good and bad.  History is filled with examples of when things got taken too far.  Some sort of damper in the feedback loop helps too, I think.  

Political movements generally do not treat kindly anything that contradicts the view they are pushing (as a means to an end).  Having an internal moral compass that goes beyond trending group-think is a safety net.  What few independent sources exist for stable moral codes should be valued, not stomped into oblivion (even if one does not fully agree with them).  Sadly to me, intolerance for religion (mainly Christianity in the US, for historical/counter-culture reasons) seems to be trending over my lifetime.  Evangelical atheism, indeed.  To it's adherents, like Mr. Bryne, it probably seems like progress against the Dark Ages.  I never saw it that one-sided, despite having spent the majority of my life as an agnostic.  It always seemed more like a turf war for power.

I will name two religious groups whom I have lived and worked in close proximity to and whom I have grown to have HUGE respect for their community and behavior: the Jews, and the Mormons (Church of Latter Day Saints).  Religious and cultural identity are enviously strong and successful in both cases.  To me, it is obvious they are doing something very right.  They are the neighbors you want.  The very definition of "civilized".