Well I'll agree with your first statement, we're on the same page there, but we'll have to disagree on everything else. at least you said it nicer than the last person who insinuated it.
just as an atheist once told me that I'm indoctrinated, I can say and believe that religious extremists have been brainwashed in their system for believing in the extremism that they do. this is kind of a nature vs nurture thing and for human beings nature kinda = nurture which is to say, you are a product of your upbringing, to a certain extent. a human being who grows up with no human contact whatsoever will have parts of their brain not fully develop and as a result, they are developmentally ill for life.
I have to do the reading on my own but right now I feel as though the passages in the holy text that come across as violent, are there to describe what to do when someone hits you first, and the more time goes by (furthering it from the time of revelation) the more of a discrepancy that comes with interpreting it for contemporary ages. the extremists will take and twist to justify what they do. but if you're right and their basis is supposed to be right, there's definitely something wrong going on and I'll say what's wrong, has to be the interpretations. And its these acts that are constantly showing up as the image of the religion itself, keeping this unfortunate vicious cycle of misunderstanding continue.
