Be sure to also read: Is God Good? (Part One).
In the Old Testament there were times when God killed nations of people at once–even all but eight people in the day of Noah and the flood–but He was still good.
The Lord gave me a metaphor to describe the steadfastness of His love and goodness within the destruction of the flood. He asked me:
If you had a farm and all the animals caught a really painful, harmful disease that was definitely incurable what would you do? Surely, you wouldn’t want them to have to go on living like that and to have babies who would also live tragically painful lives. So, wouldn’t it be more merciful for you to kill (as quickly and painlessly as possible) the infected animals before they got worse, multiplied, and infected others on the farm?
God’s goodness means He is concerned not just with the here-and-now of our lives, but with the eternal–with the whole big picture.
Something had happened in the days of Noah which caused God to take action by destroying life on the earth: there was ungodly sexuality, violence, and evil reigned continually in the hearts and thoughts of men (Gen 6). In fact, it’s so bad that God not only kills the large majority of the earth, but lowers the lifespan to 120 years so that future generations would have less time to cultivate evil (Gen 6:3).
The people were so corrupt that God in His infinite knowledge knew there was no hope for them turning to Him without His violating free will, which He chooses not to do; their hatred was too deep. They were infected with the disease of wickedness, because they choose to cultivate the wickedness of their hearts. In order that they would not multiply and produce more kids (who would be raised in wickedness and endure eternal punishment), and so they would not create for themselves even more sin (which would ensue even more judgment), God, being full of mercy and justice, chose to kill them.
This wasn’t God’s ‘plan’–He never delights in killing anyone. Scripture says that He was “sorry” and “grieved in His heart” by man’s actions (Gen 6:6-7). These aren’t the emotions of an uncaring God, but of one who is so intimately involved with His creations that their apostasy deeply saddens Him.
It made God sad that the people would choose wickedness over Him, but He could not let them dictate and infect the decisions of future generation, nor could He let them continue to destroy themselves in their wickedness. So it was in His goodness and perfect love that God destroyed and cleansed the earth with water, saving only Noah, his family, and the animals that were left with them in the ark.