Do commandments and threats negate free will?
There is a quote in the bible, " law was not created for the righteous man. Rather it was created for the sinners".
Say there is a bully who enjoys beating on you. He is exercising his free will. So according to many, there should be no law or threat against him. But to the person losing his free will to walk peacefully down the road, he may not mind if a higher power limits the bully's free will so he has more free will.
There is a new law created, thou shall not bully. This was not created for the righteous man but for the sinner. But it will apply to all, but will only restrict the will of the sinner, so he does not restrict the will of the righteous.
Atheism may relate better to the bully, since law was not created for the righteous man and does not apply to righteous. Law was there to restrict the sinners so they don't take away free will from the righteous.
If I steal from you, I restrict you free will. It is not God doing it. Free will can come in conflict with free will. Justice amounts to protecting those who will maximizes the free will of all; righteous man. The sinner reduces net free will.