2 contradicting passages in the same chapter?

There is a difference between being put to death by a court of law and killing another person for your own personal "pleasure" (whether it is anger, hate jealousy or something else, it is your own emotion that will be satisfied). You may not agree with the severity of the offense, but that does not change the law as handed down by G-d. Similarly, your lack of belief in G-d has no bearing on His existence.