"Thou shalt not murder" is not a (uniquely) biblical concept, every society throughout history has had this rule. I would have thought that would be obvious. The Babylonians had written laws against it before the jews even existed. Maybe there were societies that didn't have it, but they would have crumbled so quickly that there wouldn't be historical record of them.

I do not understand why you're bothering with slavery at all in your argument. Yes, slavery in ancient times was different from the kind practiced by Europeans and Americans in early modern times. I don't think anybody here said otherwise, in fact I think that it's more or less common knowledge on this forum. It's still slavery regardless.
As for the "atheists don't have any basis on which they can condemn slavery" argument - I'll get to that later, but now I'll just point out that christians have used their religion to both justify and later on condemn it. Of course you might respond by saying that the christians who held African slaves were bad christians who didn't follow God's will or whatever. Which sort of makes an objective moral standard like "Will of God" kind of useless, because evidently the content is a matter of subjective opinion.

Various European philosophers have put forward their ideas of the "social contract" which gives a plausible explanation as to why people have rules and bother following them. Hobbes is my personal favourite, but there's also Locke, Rousseau etc.

And there's the evolutionary aspect - like you said, atheists generally see thoughts and emotions as nothing more than complicated electrochemical reactions. Even in the total absence of religion people would still follow social rules and their "conscience" because humans are built like that. Some christians, like you, think that atheists can turn into killers overnight because they have no rational reason to follow the dictates of their consicence. But it doesn't work like that - knowing that empathy and conscience are biological functions doesn't make them any less potent. Sure, there are sociopaths, but that's a condition not caused by voluntary choice.