The problem is due to willing ignorance of the biblical scriptures.
In the situation(s) you refer to there were specific reasons that God gave the commands He did, and they were one time commands for each instance. For example, there were people that made stone statues and heated them to high temperatures and then burned their children alive on them to their "gods" a sacrifices.
Another misunderstanding, due to willing ignorance, is the penalties for sins. In many cases the penalty given is death. What needs to be understood is that these were the maximum sentences allowed and not mandatory sentences. Look at most existing legal systems - the judge determines the amount of penalty after the trial, and it is rarely ever the maximum allowed by law. Jesus gave us a good example of this. The woman that was caught in adultery was not stoned to death, but warned to discontinue her sin.
I find it interesting that when a Christian does something wrong that other Christians publicly condemn the act. When Muslims do something wrong other Muslims are silent. If a Christian shares their beliefs with another person and the other person rejects what they are saying they go their separate ways. If a Muslim shares the Quran with another person and they reject it he can kill him.
My scriptures tell me that Satan came to steal, kill and destroy. I don't see a personal God of love in the Quran, I see Satan.