Here's a possible view:
I heard a story that the human genetic line had become impure and corrupted due to the inbreeding with demonic entities and that these 'pure innocent babies' were in fact not so pure at all but just younger versions of the genetically corrupted men/creatures/beings he was destroying.
It seems that God was not even dealing with normal humans any more but something else that had become genetically altered.
Mankind’s depravity had reached a level that evil entirely permeated every part of his being. His wickedness was great- that is, his actions were wicked. Every imagination was evil - his mind was wholly corrupted. Every thought of his heart – his will, his desires, his emotions, his passions, had all become so sin stained that there remained nothing within them that was not evil. These people upon whom God poured out the Flood were not merely dabbling in sin here and there, everything that they were doing was an horrific abomination!
“The earth also was corrupt before God, and the earth was filled with violence. And God looked upon the earth, and, behold, it was corrupt; for all flesh had corrupted his way upon the earth. And God said unto Noah, The end of all flesh is come before me; for the earth is filled with violence through them; and, behold, I will destroy them with the earth.” (Genesis 6:11-13)
The Earth was corrupted and filled with violence! There is a linguistic device employed in Hebrew that we see throughout the Old Testament, and that is emphasis through repetition. Whenever a word or phrased is used repetitively, it indicates a stronger or greater degree of the expression. The evil depths that the people who lived before the Flood had sunk to is strongly emphasized and amplified here in verses 5, and 11-13.
In considering why God sent the Flood, we must first realize that those living upon the Earth were completely and utterly wicked beyond the hope of changing. There were no innocent bystanders caught up in the Flood.
“If you had the opportunity to go back in time and kill Adolph Hitler before he became Chancellor of Germany, would you do it?”
God knows exactly what the world would have been like in 1940 if Hitler had not survived to become Chancellor of Germany. If we knew what God knows, if we had all of the facts as He does, would we find fault with God if He had chosen to end the life of Adolph Hitler in 1920? I don’t think anyone would dispute that. Would it, however, become more objectionable if God chose to end His life, say, when he was 20? 15? 10? Remember, we KNOW beyond any doubt the terrible evil that Hitler will commit if he is permitted to survive until he takes control of Germany, so when exactly would be an acceptable time in his life for judgment to come?
So if:
“The earth also was corrupt before God, and the earth was filled with violence. And God looked upon the earth, and, behold, it was corrupt; for all flesh had corrupted his way upon the earth. "
Then there is no such thing as an innocent baby.
I guess when you want to terminate vermin like roaches you have to make sure you exterminate all the young and eggs as well.