Do "holy books" have a negative effect on morality; do they do more harm than good for society?

This is atheist says, indeed they do have a negative effect and they do cause far more harm then good for society. Especially considering the most common "holy books" are books like the Bible or the Koran. These books have some horribly brutal, barbaric and primitive allegedly god-given moral instructions. Sure, there are a few good moral instructions, but like Thomas Jefferson said, these are like diamonds in a dunghill. The likelihood that deranged religious people will take the wrong "holy book" endorsed morals seriously is too high and there is no proviso about not taking them literally. This is why there is so much religion inspired violence and social disharmony in the world today; simply because religious people take their "holy books" too seriously, right? They lack the reasoning to determine right from wrong and this means the religious moral instruction they received as children was simply a bad moral instruction, doesn't it?