In atheist circles, it is dismayingly common for atheists to say: "Fundamentalists are, arguably, more true to religion than the moderates. Fundamentalists take the entire Bible seriously. Moderates, on the other hand just cherry-pick the parts of the Bible they like, and call the rest metaphor. But if you allow part of the Bible a metaphor, on what basis can you discern the literal from the metaphorical?"
First of all, there are some parts of the Bible that are quite obviously meant to be metaphorical: Jesus' parables, or the phrase "lamb of God". And there are some parts that are quite obviously meant to be historical: all those boring genealogies (though I would not trust their accuracy). I say it's obvious, but on what basis? It's on the basis that I can read. On the basis that I'm not stupid.
The rest of the Bible is less obvious, but that doesn't mean it's impossible to determine the genre of specific parts. For one thing, the Bible is not the only religious authority. There is tradition. The Church (especially for Catholics). Theology and Natural Theology. Or, if you like, you can ask God. No, I don't consider these to be legitimate authorities on anything I'd call "truth", but their authority is at least as legitimate as the Bible's. In what sense is it more "true to religion" to take the Bible's literal word as authority, as opposed to taking the teachings of the Church as authority?
If you want a more legitimate authority, you might try the study of history. I'm not much of a history person, but I believe in historical evidence. Just because it's one of the humanities doesn't mean you can't determine historical facts with a reasonable amount of certainty. When we disagree with historical revisionists like the Holocaust deniers and Afrocentrists, it's not because we simply dislike their political motives, but because they are actually incorrect, as determined by historical evidence. Historical evidence can be used to determine the context of the Bible. Who wrote it, when, with what purpose, within what culture, translated by whom, etc. From this, we might determine the relative reliability and authority of different parts of the Bible. I don't know any details, because I find it all rather boring, but at least I know that the field exists.
The atheists in the audience might ask, "Doesn't the fact that the Bible was written by flawed humans contradict the idea that it is the word of God?" Not really. It can't, because "word of God" is one of those vague waffly terms whose meaning is widely disagreed upon. In any case, it is far more obvious that the Bible has a historical context than it is that "Word of God" means every word should be taken literally.
My point is that it is possible to discern the good from the bad in the Bible, and there's no reason to take an "all or nothing" attitude. We ought to acknowledge the possibility, so we can move onto the real problems. The real problem: historical study of the Bible has been unduly biased. If anyone thinks the Bible is reliable evidence of physics-defying miracles, that's an obvious sign of bias. Second, normal everyday Christians are ignorant of any sort of Biblical scholarship. They simply assume that history backs up whatever they already believe. Or worse, they find a few biased experts who agree with them. Third, those who take the Bible metaphorically usually assume that it is morally instructive (or instructive in some other way). Perhaps this is sometimes true, but one needs an outside source of morality to determine which parts are good and which aren't.
More generally, I dislike some atheists' attitudes towards "moderate" religion. They seem to think that moderates somehow reduce to, or are a lesser form of fundamentalists. All this despite the fact that most of us would obviously prefer it if all religion were more "moderate". Moderate religion is often considered to be a "shifted goalpost" from fundamentalism. But goalpost shifting is only wrong when used for convenience within a debate; here the shift is the result of a long historical process. Besides, it's the fundamentalist movement that is relatively modern.
And regardless of whether moderate religion reduces to fundamentalism, the argument is about as compelling as an apologist arguing that atheism is a lesser form of nihilism. That is, you're trying to be charitable, but you actually end up making a straw man. I am in favor of directing much criticism towards fundamentalists and evangelicals, as well as making people aware of how large, powerful, and dangerous the fundamentalist faction is. But if your target is moderate religion, please argue against people's actual beliefs, not against the fundamentalist beliefs that you think are so much "better".