For example, you read in the Bible that newborn babies should be mass-slaughtered just because of their parents' sins, and then if you're a "true believer," you'll try to bend your conscience to match that.
Uhrg. What are you even talking about? Where did you get that from?
Look, tons of religions have manufactured their own specific ways of worshiping, and they use those patterns to shape people's consciences. Just like how an SS officer's moral compass was totally warped by Hitler's ideology, religious doctrines can have that exact same kind of psychological grip. Religious wars, the Inquisition, colonial atrocities... religion is lurking behind all of it.
Official religion breeds this spirit of self-righteousness and can basically trigger some mob to go out and start a massacre.
The history of the Jews and the wars fought by ancient Israel is a completely different story.
A truly Christian-trained conscience won't allow for killing—if it’s actually been trained that way. And it's only "trained" if there's actual truth behind it. You can't build a genuine Christian conscience on fake teachings about the Trinity, immortal souls, hellfire, and stuff like that.
Maybe the phrase 'training the conscience' sounds a little silly to you.
If you actually looked at the conscience as God's tool for telling good from evil, you'd see that the tool is totally broken. Basically, the world is showing us a picture of humanity with a massive, global case of a broken conscience...