It's different when you bring God into the picture though, isn't it?
It sure is. And the difference should help you with some of the doubts and issues you have. God is greater than we are and can do what we cannot. This should be a source of comfort and assurance.
God isn't limited to just two choices. He can make the trolley turn to mist, or make the children fly away.
What if a greater good is achieved by Him allowing the one to die than would be achieved by turning the train to mist or giving the children wings?
Turn it back to the Amalekites. What if the command to destroy them achieved a greater good than would have been achieved had He let them just continue to terrorize people?
If we're talking about God being put in this position, then we have to consider all the other things that he could do. If those other things that he could do mean not letting anyone die, and yet he chooses to flip the switch and kill one person, then he wants someone to die. Why does God want there to be such unnecessary death and destruction?
Very good question. A very good one.
I immediately think of Jesus. Why would God subject His Son to such torture, torment, abuse, and humiliation?
Why would God allow His righteous Son to die at the hands of evil religious people?
One reason is because God loves us. Entailed in this is that He allow us the freedom to love Him in return. But where love can be returned, it can be withheld.
Through the death of One Man, Jesus of Nazareth, salvation was made available to billions.
There is no more clearer example of a morally sufficient reason for allowing untold suffering and anguish than this.
Taking it back to the Amalekites for a moment.
God loved them. This means that He allowed them to return their love or withhold it.
They chose to pillage, murder, harass, and generally live lives of total disregard for people. They did not love God and God let them live for a long time. He gave them time to change and they could have if they wanted to.
God also loved the people who the Amalekites would raid and rape and pillage from. He loved the children and women who would be raped by the Amalekite warriors, some of which would have been youngsters, trained in war and brutality. He loved the babies who the Amalekites would dash against walks and burn as sacrifices.
God loved the one's committing the evil and those receiving it.
God being Holy, after so long of waiting patiently, decided to defend the helpless and the weak and do what was best for everyone, even the Amalekite children. He ordered them to be cut off from the land of the living like a gangrene limb is cut off to preserve the body entire. It grieved God to do this. He wanted them to repent. But they were not willing.
So what about all the Amalekite babies?
First of all, I doubt there were any babies killed. In fact, later on in Israel's history, we see the nomadic Amalekites still around, a thorn in Israel's side even after Saul attacked them initially. Israel had not utterly destroyed the Amalekites because many of them were still alive. It was customary wartime practice during this period for those about to be attacked to see to it that their non-combatants, babies and the like, were removed from the place of battle to safety. Had any been left alone or abandoned when the Israelites attacked, they were to have been mercifully killed to spare them the manifold ills that would have come upon them from exposure.
God gave these people some 500 years to repent but they were unwilling.