I think you misunderstood stand the quote, evil within the quite is not what one side considers right and the other wrong, for example as you see with issues such as abortion, but instead actions both sides morality think are wrong. Religion allows people a get out clause for committing an act they themselves would otherwize know to be wrong, murder after all is wrong in most religions, yet people will happily go on a killing spree on the belief god wanted them to do it. The belief in god in no way is providing them with a morality that says killing is fine, religion simply features the ability to override morality by attributing it to a higher power.
Hence when he mentions good people doing evil things, he refers to people committing acts they know themselves to be wrong, justifying it on the basis of a "god" commanding them to do so.
Religion allows people to ignore there own morality, without religion and a god though, where people are accountable to themselves rather than a higher power, going against your morality is far harder to justify.
In reference to you last point, statistically the higher the atheistic population of a country the lower the homo side rate and amount of conflicts it engages in. (if you not come accross it ill spend a few mins looking it up if you like)






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