Their society was comprised of Christians. Sometimes their leaders were popes and others in authority with the churches.
And many, many many of those leaders went against the explicit teachings of their own Church. Again, their religion told them one thing, society told them another. They chose society's influence over the Church's.
But the character who was the most vicious was a god capable of sending even well-behaved non-believers to eternal punishment in hell.
I and many other Christians going back over the last 2,000 years of Christian history would dispute the idea that "well-behaved non-believers", as you call them, go to Hell. Some of the most influential and significant Christian theologians of all time have disputed this idea, including St. Gregory of Nyssa who lived in the 300's and St. Isaac the Syrian who lived in the 600's. Orthodoxy has never firmly said who will and will not go to Hell, as that is not our job. Catholicism has speculated about it, but even in the most confidently-worded of Papal bulls, there has never been any dogma concerning it.
Non-violence isn't a "core virtue" in all Buddhism.
It absolutely is. It's one of the Five Precepts, and if you kill anyone or anything, it is very likely that you will reincarnate into a hellish realm for a few centuries or even millennia.
Ahimsa - Wikipedia
Conscience doesn't make moral rules: "One should not drink alcohol" is a moral rule created by the reasoning function of our brains. Conscience is an unconscious intuitive judgment (See Jon Haidt's research) It makes judgments case-by-case.
Yes, conscience doesn't make moral rules. It is influenced by the moral rules that we have internalized as being true.
I doubt you're right on that, but I'll grant it for sake of argument. So what?
If you have cultural biases (which you do, I do, and everyone on the face of this planet does), then that influences how you think of moral questions and questions of conscience. If one is aware of their own cultural biases, then one can start to be aware of how their own biases affect how they perceive the world and matters of right and wrong. If one is completely unaware of their own cultural biases, as seems to be the case with you, then they will think that their way of looking at the world and questions of right judgement is the natural way, the only way. In this case, you would be no different from the Salafi Muslim who thinks that his religion and his morality are as clear as 2+2. A Salafi Muslim would be calling you out on your judgement being warped by secularized Western culture.
I can say it because conscience is the only moral authority we have.
You mean aside from all the manifold factors that inform conscience?
If the mind is unbiased, the judgment of conscience rules.
There is no such thing as an unbiased mind. And even if there was, you have no grounds to say that your secular Western mind is any more unbiased than that of a Salafi Muslim or a Burmese Buddhist or a Russian Orthodox Christian or an Israeli Jew. We all have our biases. The only question is whether we're aware of them or not.
I think even the Catholic Church bows to an individual's conscience when its moral guidance is questioned.
I'm not sure what this is supposed to mean.
In the moral situations I face, I rely only on conscience. If an act feels wrong or feels unfair, I don't do it. It's obviously a lot more difficult than that, but it isn't difficult to understand.
And what feels wrong or unfair to you is a result of how you have been conditioned by society, your family, your education. your personal philosophy and your belief systems.
The part you won't agree with is that any creation of the reasoning mind is a potential bias. For example, the Sixth Commandment is the product of a reasoning mind. If a Christian interprets that commandment to believe that killing is always wrong that belief will form a bias that will conflict with conscience given the facts in a clear case of self-defense.
And my point is that you have absolutely no way to tell what an unbiased conscience would do, since every person, every society, every religion on the face of the planet has its own set of biases that affect our conscience. Even babies are already being indoctrinated into the biases created by their family and their culture.
So how can you define what an unbiased conscience would do
when such an unbiased conscience doesn't even exist?