... and their unborn or young children he drowned in the Flood. Aside from the Original, what sin could they possibly commit?
Ok, let's stay with the Christian worldview then.
So the children of the flood....the innocents.....why were they harmed.....why were they taken?
First off, we don't know for certain that they did experience pain and harm in the flood....we don't know.
We do know that given their innocence they immediately left this life and went to dwell with the Lord forever in his kingdom.
What if that final generation of reprobate and their innocent chidren had been allowed to continue on? The same innocent would've been lead into reprobation and evil by their forefathers exactly like the generations before them and the generations before them, etc.....The Lord allowed the world's sin to come into it's fullness before judgment was passed. If the older, reprobate generations were taken and the innocent children left behind they would've experienced a miserable existence in which they have to contend with everything on their own while dealing with deaths of everyone they ever knew (regards of how evil they were). And God would be criticized for that situation as well.
The children of the flood were spared eternal separation from God because of their innocence and spared an earthly existence in which they would have to fend for themselves with nothing at their disposal.
If you criticize God yet stop at the point of human death you've invented a non-Christian worldview to play off of. You have to allow the entirety of the situation to be considered in order to represent the Christian worldview correctly and that entails stepping into God's eternity.