Here, let pastor Joe explain this to you. God is omnipotent and benevolent, meaning that he knows everything and he has your best in mind. Obviously you know that.
However, a parent is benevolent to their children. They don't want them to get hurt. HOWEVER, they will still let them ride a bike with the potential of falling over, and when they get older they can still drive with the potential of wrapping their car around a pine tree.
God's permissive will allows people to kill eachother. If everything went by God's perfect will, like Heaven does, then nobody would kill anybody because the bible says "thou shalt not kill".
Unfortunately I can't make it any simpler. *sigh*
EDIT -
Sorry for coming off as a jackass. =)
EDIT -
Also, you've got the Jewish punishment for breaking a commandment. In Christianity, there is no punishment for breaking a Bible law, asuming you repent. Being cleansed from sins is simple.
Romans 10:9-13:
That if you confess with your mouth, "Jesus is Lord," and believe in your heart that God raised him from the dead, you will be saved. For it is with your heart that you believe and are justified, and it is with your mouth that you confess and are saved. As the Scripture says, "Anyone who trusts in him will never be put to shame." For there is no difference between Jew and Gentile—the same Lord is Lord of all and richly blesses all who call on him, for, "Everyone who calls on the name of the Lord will be saved."