Adams,
It is important to understand the basic concept of the Torah obligaiting us to administer capitsl punishment for people who violate certain egregous sins. The Torah prescribes a very unlikely scenario that must occur, before we actually put someone to death. The two witnesses must warn the person, within seconds of the sin being committedthat if they go through with the sin they will be killed by Bais Din (the Jewish court). The person must respond to the witnesses that he is going to do it anyway. Obvoiusly, this is a highly unlikely scenario. Rav Chaim Voloziner explains that the reason people would respond affirmatively to the death warning is because they crave proper atonement for their uncontrollable sin.
Maharal explains that the punishments of the Torah are not meant to be a practical deterrent to sin. That is the task of Bais Din in each generation.
Rather, the Torah mandates a death penalty in order to represenet the totality of what human activity should entail, which includes punishing those liable for punishment. However, it is not intended as being a prctical deterrent.