The Bible is divided into several dispensations of time in which God deals with mankind in a certain manner. It can be understood in this way. What applied for Adam and Eve was a bit different when it came to setting up a nation of ex-slaves who were a bit barbaric. Harsh punish for crime is the best deterrent for crime as we have seen in other nations that have far less crime than we who are tolerant.
The governing body is given the exclusive right to pronounce a death penalty for criminal acts. The Bible says obey the law of the land.
In accepting the laws of God, and becoming God's people, Israel was attempting to become a holy nation before God while on earth. Notice that stoning or other forms of death penalty were not as much a punishment for crime but to put the SIN out of Israel, in this way, they maintained their holy status. This brought a much stiffer penalty for sin. Their penalty was suffered in this life. Man's penalty today in suffered in the next life or Hebrews 9:27 And as it is appointed unto men once to die, but after this the judgment: At any rate the Romans 6:23 says For the wages of sin is death; this death is separation from God for all time, that is forever in a place that burns with fire, forever. Stones are to be desired rather than this. People who did not know anything about this place have had experiences that demonstrated that this is a spiritual reality for the place of the spirits of men who have separated in death from their natural bodies.