Isn’t the real problem deeper than the content of any particular set of beliefs that have coalesced to constitute one religion or another? Scratch the surface of pretty much any religious texts and (with the possible exception of Jainism’s Aganas) you’ll find some nasty stuff, as you will some benevolent stuff too.
The question surely is what people do with moral narratives. Call it “moral philosophy” and you have ideas about how to live a good life that are reasoned but tentative, provisional. They’re change-apt as new and different thinking comes along. Consequently not many people will die (or kill) over the differences between, say, Aristotle and Plato.
Call it “religion”, "faith", “revealed” etc and claim it to have been handed down by a morally inerrant god though and the narratives become certain, atrophied, unchangeable no matter what. That is, they become dogmatised.
And the problem with dogmas (not only religious ones by the way) is that not only are they certain in their content, but that people who subscribe to them are certain that they’re right to do so. And once they’ve got themselves to that position, why then wouldn’t they die – or kill – to defend them, or to propagate them? After all, when in your head you know – really, really know – that if you don’t convert someone from his heathen ways he’ll go to hell, then it’s positively your duty to do the converting. You’d be acting immorally if you didn’t!
And where that leads is pretty much to what we see today– silos of certainty, some of them outright hostile to the others, some of them paying lip service to tolerance but hey, you know, we’re still right and they’re still wrong when all said and done.
As to what we do about it, in a word: education. Not education that religious claim X is right and religious claim Y is wrong (or vice versa), but rather that reason and scepticism and the ability to detect and reject bullshit arguments matter. Really matter. Even when the theist espouses reason altogether by claiming faith to trump reason or some such, that in itself is a bad piece of reasoning.
Will that ever happen, either at all or before someone with a “holy” text in one hand and the nuclear codes in the other has his way? Who can possibly say, but it’s worth trying I’d have thought.
How about teaching philosophy in primary schools and making it as compulsory as English and Maths at least until GCSE stage?