One major problem that people often have in looking at situations like babies dying in the Flood or being killed at God's command is that you aren’t looking at how God’s perspective differs from ours. God can see all of history, not just one moment of it at a time. He can see how every action and inaction affects everything else down through time.

Also, God is interested in eternity, not so much our time on earth. We tend to think of our life on earth as the main part of our existence. But to God, our time on earth is merely the beginning of an eternal existence. It’s a drop in the bucket, a speck, a mere second compared to the rest of our existence in eternity. And it’s eternity that really matters. God’s purpose is to have as many people as possible freely join Him in heaven for eternity.

So, considering God’s perspective, if someone dies early or dies a painful death and more people end up in heaven because of it, it is good. If a baby dies and goes to heaven rather than growing up to defy God and go to hell, that is good. If one person goes to hell and two end up in heaven because of that, it is good. We can’t see all of the effects of the things that happen here on earth, but God can. So until you can see with God’s perspective, you have no call to judge any of His actions.