You are reading scripture from a God, not a man, and this God speaks of spiritual things using early illustrations. This scripture says "my Father's house" and it speaks of Israel, not an individual.
Are you saying that because you don't believe in stoning that you question all of scripture?
As I made a study of scripture telling of stoning in the OT, I found that there were many laws that protected people from excess stoning. It was done in the same way we give the death sentence to criminals today. I also found that it is a message to us about what God feels is important for us. It is a basic rule of the Lord that we are to respect life and never take it based on what we think, it must be decided by appointed rulers.
I do not understand about stoning, but I do understand we are created by a God who loves us and wants us to live, not only on earth but etermally. I don't believe my not understanding how this God can ask for stoning, but I do not give up my faith because I don't understand.