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My position is the default position and perfectly in line with science.

Fair enough, I was working with a narrower definition of atheism.

and faith is bad.

And there's an unfalsifiable faith-based assumption. I now have no way of objectively interrogating your statement (and therefore, your entire position). However, based on other subjective (moral and otherwise) assumptions we agree on, we can subjectively interrogate whether this statement makes sense. Do you see the difference? There is something such as non-objective interrogation, and frequently there's no other alternative (you can't objectively justify the scientific method, for example). Also for the sake of internal consistency, I hope you hold the same position regarding, say, philosophy.

Because the answer can be used as justification for atrocities ("we are good chosen, we were given the land").

I assume you're referring to Zionism in your example, in which case you should know that Zionism was a secular ethnonationalist project, and that its leaders were predominantly atheist. These guys did not give a shit what the Torah said. It'd be generations after Ben Gurion that religion would be an important part of Israeli politics. Besides, there's nothing that can't be used as a justification for atrocities; blaming religion in particular is naive when you have an event called the Football War.