God reserves the right to wipe out the entire population of the planet (in the past by flood, in the future by fire.)
Who are you, oh man, to question what God does with His own creation?

While God is very loving to His family, he is very ruthless to those who threaten His family.
Anytime you see what you consider "atrocities" in the Bible, that is what is happening.
God is like a mama bear. Don't threaten His cubs!

(Of course the only threat He is usually concerned about is a spiritual threat. His cubs tend to get killed a lot physically, but that is not much of a concern because He can give them new physical bodies whenever He wants.)

Abraham knew that God had promised to make a great nation through Isaac, so He trusted God to do that regardless of what he was asked to do in the mean time. It only seems outrageous to you because you do not know and trust God like Abraham did.

Here, let me give you the exact words of Jesus about how God looks at weeds in His garden:

Jesus told them another parable: “The kingdom of heaven is like a man who sowed good seed in his field. But while everyone was sleeping, his enemy came and sowed weeds among the wheat, and went away. When the wheat sprouted and formed heads, then the weeds also appeared. “The owner’s servants came to him and said, ‘Sir, didn’t you sow good seed in your field? Where then did the weeds come from?’ “‘An enemy did this,’ he replied. “The servants asked him, ‘Do you want us to go and pull them up?’ “‘No,’ he answered, ‘because while you are pulling the weeds, you may uproot the wheat with them. Let both grow together until the harvest. At that time I will tell the harvesters: First collect the weeds and tie them in bundles to be burned; then gather the wheat and bring it into my barn.’”

We don't seem to find a moral problem with weeding a garden, do we? Why can't God weed His creation? He is much further above humans than a farmer is above his weeds. (I suppose that if you are a weed, you might object.)

There is a much bigger battle going on here behind the scenes and humans are pretty much expendable chess pieces belonging to two different players. For His own reasons, God has allowed Satan, a mere creature, to play a game against Him. Sometimes God wipes out Satan's forces en masse. Sometimes Satan is allowed to win a battle.

You cannot judge God. You don't have His perspective about what is going on. But know this. Anyone who is killed for any reason can and will be reinitialized on the chessboard the instant God decides to do so.

Sometimes we humans put too much emphasis on these temporary "avatars" (physical bodies) we have been assigned. Flesh is expendable and God has and will reinitialize them at any time he pleases.

This is God's matrix. When your avatar gets killed, you wake up in His presence. Then, when the time is right, you go back into the game with a much more powerful avatar - if you are one of His cubs.

I'm personally looking forward to my upgrade to Stan 2.0. :o)