I can understand that you wonder about the goodness of God in this story. Judging by modern standards, we could explain it by saying that these were primitive people with a primitive understanding with whom God was dealing.
But I wonder if today we are any more sophisticated or moral, what with multiple wars and slaughtering of innocent civilians, reluctance to go to the aid of starving or warring nations and a general lack of respect for creation.
With that thought as a backdrop, let's look at the situation in this episode.
To appreciate what happened, we have to understand a little about the Israelites' service to God. God had made a covenant with the Israelites to be their God, taking care of them while they would be God's people.
This entailed certain obligations for the Israelites. Among them was the duty of responding to the call of a charismatic leader to go to war. It tested their loyalty to God and faith in God leading them into battle.
Obey the covenant
The number of fighting men and the kind of weapons mattered little for God fought for them. This covenant relationship bond with God was primary and it was reaffirmed at various intervals.
After Moses, during the period of the judges, the Israelites were organized in a confederacy of 12 tribes, sons of Jacob and their descendants.
Samuel was the last judge and it was under his guidance that Israel went from the old type of charismatic leadership to a new prophetic leadership and from an inadequate tribal confederacy to a more stable monarchy.
The change to a monarchy seems to have been grudgingly granted to them by God. It meant that Israel would become like the other nations, undermining its distinctive character.
From earliest times, Israel had been bound together, not by race or economics, but by its relationship to God who was their king. Israel was not a nation but a people, and the fear was that the adoption of a monarchy would threaten its special character as the "people of God." To offset this possibility, there arose prophets who kept Israel aware of its special destiny.
Saul lived in this transitory period when the tribal confederacy was still the model. He, like the judges before him, received the "spirit of God" and was endowed, in a special way, with leadership authority which enabled him to deliver the Israelites from the enemy.
His first act after his anointing by Samuel was to summon all the tribes under threat of death to do battle against the enemy. Saul's victory was evidence of his charismatic leadership and so the people chose him as their king.
In war, conquerors usually take whatever they want from those they defeat. But the Israelites believed these to be holy wars commanded by God. As a result, the spoils of war were considered herem, that is, belonging to God totally and so had to be completely destroyed. To take anything, for whatever reason, would be "breaking faith" (Joshua 7:1), an offence against God's holiness. This is what Saul did by keeping some of the spoils.
In view of his covenant obligations, therefore, Saul was punished, not for sparing lives but because he had used his own judgment in deciding how far to go in obeying God. As the king, his was an act of disloyalty that tainted the Israelite community.
Because Saul was passionate in his devotion to God, this rejection by God through Samuel preyed heavily on him. As a soldier doing battle, Saul does not seem to have been gifted with the profound insights regarding the nature of Israel's faith, as was Samuel. He begged for pardon but that could not deliver him from the consequences of his action.
As we read this story of Saul from the perspective of the covenant of the people of God, we begin to understand their situation. With their belief in God's continual and vivid presence among them, they consulted God every step of the way, placing their trust totally in God, not in their own power.
This story could serve as a powerful motivation for us, especially in the season of Advent. In what or whom do we place our trust? Is it in our material possessions, our strength, our riches? Or is it in Christ who became one of us 2,000 years ago?
Reflecting on this story, we can become more aware of God's continual presence. We can understand God's love for the people of Israel and how much God cares for us as well. We can strive to seek God's guidance as we carry out the divine will in our daily lives.