They all revolve around the bible and how Catholics read it. I talked about it before. There is a big difference between Christians in the way they read the bible. Protestants set the bible as the highest authority. That means they try to put the actual words of scripture over and above any Christian tradition. That means the way the bible has been interpreted in the past is informative but not normative. So they can't use Christian tradition to declare one part of scripture less important or one way of reading scripture to be wrong.
Catholics say God speaks through sacred tradition just as much as He speaks though the bible. We have one faith. We can agree on the questions that are important to the faith because we believe the pope will not lead us into error. That means we can also progress into a deeper and better understanding of God's truth. Not something that completely contradicts the past but something that clarifies things for the future.
So how does this change the way we look at some of the passages atheists love to quote? First of all, it becomes very important that the church does not frequently call our attention to these passages. It is not because the church is trying to cover up the embarrassing bits of the bible. It is because they are less important. They are not the centre of the faith. They are a footnote. Protestants can't really say that because the bible is the bible to them. They can point out that nobody is teaching these passages as something to be imitated but they say that teaching from scripture is beneath the scripture itself in authority so that does not quite work.
Secondly, we have this idea that God's relationship with man progresses. God's grace increases with the various covenants but also over time within the same covenant. So early on we have the story of Noah. God kills every man woman and child on the earth except for eight. He does this as punishment for sin. There is still grace. Noah and his family are saved. Still it seems pretty harsh. God says as much. He promised to never do it again. But why did He do it once? The wages of sin is death. We all need to understand that we interact with God as death row inmates who have received a reprive. We should not be confused about why God wipes out sinners. We should be confused about why any are saved. That is the way the story is told. That the salvation of Noah and his family was the remarkable part. A sinful society completely wiped out is unremarkable.
God continues to teach us that sin causes death but over time uses less and less actual death to do it. There are three ways of dealing with evil.
- Kill the evil people. This happened a lot early on. The people of Israel need to be made holy. That required they be given a special land. That land needed to be free from heathens or the Israelites would have just degenerated into another heathen nation. So God told them to completely wipe out those nations. Many heard there would be no mercy and knew they had to run far. They could not go into the hills and come back in a year. They had to go hundred of miles and never come back. It was brutal but God wanted a people for Himself and He knew evil would not easily be kept at bay. It would require raw power.
- Separate evil people from your chosen people. This is racist although not completely. Members of other races could convert to the Jewish faith. Still God separated Jews from gentiles using a bunch of ceremonial laws and practices. Circumcision, dietary laws, laws around washing, animal sacrifices, Sabbath observance, laws against intermarrying with gentiles or even sharing dishes with them. These protected Jewish society from many outside influences over the centuries. Still Eleazar died because he refused to eat swine flesh. 2 Mac 6:31 says he died "leaving in his death an example of nobility and a memorial of courage" but it is strange because Christians today eat swine flesh.
- Overcome evil with self-sacrificing love. This is the way Jesus showed us. It requires the grace to be able to look evil people in the eye and love them even knowing they might kill you. This is what Jesus did and what the grace of God's word and sacraments is supposed to enable us to do. The ceremonial laws are gone because God does not want to protect us from evil people. He wants us to engage them because we now have the means to be able to win the spiritual battle. Sin still causes death but it is our death. The willingness of all Christians to give themselves as martyrs.
So saying it was OK for a pope to call for a Crusade in the 11th century does not mean it is OK for a pope to do so today. Not just because people are less likely to listen to the pope today but because the Holy Spirit has moved us beyond that. Not saying it was wrong but saying organizations like the United Nations are the appropriate ways to do a crusade today.
So no matter how many people God allows to be kill and why He kills them He cannot murder. In fact, all death is allowed by God. We question it all. The point is none of us deserve to live. We continue to draw breath by God's grace. Why does He let 20 children die? I don't know. But to accuse Him of murder is to confuse things greatly.