While I would like to believe that it's because we are good, moral people trying to do the right thing, that isn't why we didn't kill Saddam.
Capturing him and putting him on trial helps us with the "hearts and minds" aspect of the war. If we put a bullet in his brain, it would certainly be him getting what he deserves, but he would also become a martyr. Since we aren't the home team in Iraq, the Baathists, insurgents, and outside forces with anti-US leanings would have a field day creating propoganda accusing the US of all kinds of terrible things. Since we claimed the moral high ground, it becomes tougher to convince people otherwise.
Secondly, by involving the Iraqis in the death sentence of Saddam, we are trying to help them take ownership of the changes going on in their country. If we kill Saddam, then he is a casualty of war. If they sentence him to death, the people have launched a sort of democratic coup. Perhaps because Iraqis sentenced their own former leader, they will feel more pride/duty concerning the new direction of the country.
Hope that helps!