Couple quick points.
1. In Regards to God Killing cities of innocents. It states in the bible when Abraham asked God if he would spare Sodom and Gomorrah if their were 50 Innocents, God said yes. Abraham kept asking this question finally getting down to 10. And God said he will spare the righteous. This was also shown to be true when the Angels came and spoke to Lot telling him to take he, his wife and two daughters away or they will be wiped away with the city.
2. Also, when citing some of these killings, it is best to actually read the whole context of what is going on. For example when Joshua was ordered by God to wipe out every man, woman and child in Canaan. People will say how God wants to kill innocent people when if you read further, states that the people of Canaan where sacrificing their children by burning them for their own gods they believed in.
3. Another popular one is the whole bash babies heads against stones somehow equates to abortion. When in all reality it is a call for revenge from the Israelites. It was not coming from God.
4. In regards to Christianity. one of the points of Christianity is that Jesus gave his life to atone for the sins of man. All Men are created with sin. No one is truly innocent and if you accept Christ as the savior, you can be forgiven for your sins.
5. The Old Testament Law. Galatians 3:15-29 explains part of this. The gist is that The Law was put in place as a guide until the coming of Jesus that Abraham was told about. That once Faith came about that guidance under the law was no longer what was necessary to enter heaven. When Jesus speaks about not getting rid of the law but that he is here to fulfill it, I take that to mean that he is here to fulfill the prophecy of his coming and that the law was no longer the way into the kingdom of heaven . Also most of the old testament laws were actually laws of the land and culture of the time.
6. And my last point for now. What is logically wrong with a just and loving God. Can a parent be both just and loving? Can I love my child and still discipline them when necessary. Can God love his creation but also punish them when they disobey Gods law. If you notice that after Christ came that the Mass destruction of cities ended. I believe this to be because Jesus gave his life for the sin of man. That Christ would accept the responsibility for the sin of man if they would believe in him and believe in the word of God.
Like I stated before, i am a former atheist so i get why you have a lot of questions. I also get why it is hard to believe in a Creator God. Just because I do believe does not mean I believe in a young earth, that I deny evolution or totally disregard science.
I will try to come back and reply to more of the God killing sprees brought up on here. But keep in mind that whatever contradictions you may find in the Bible, koran, torah...etc... that still does not logically rule out the existence of a Creator.
I am not posting to try and convince anyone to believe in God. In my opinion that is for you to do for yourself. I just want to try and demonstrate that some people do put some time and effort into their belief. I still read Atheist books, magazines, articles as well as Religious books to try and get a better understanding of my faith. I still have plenty of questions and will continue to look for the answers.