This was the exception to the rule. God killed for the least or greatest offense, with prejudice. Starting at Numbers 16:30, you will read how God killed folks for . "wicked" people as you might say. The Isrealites are scared because of the spectacle, and complain about how Moses had played a part in the execution. So, God killed 14,700 Isrealites by plague for complaining. It was really a heartless act, as these people were confused, scared, and sad. It is perfectly normal for a person to feel anger towards the judge who puts their guilty son in the chair. God had no mercy in this case.
How can you say this for sure? Let's look at this from a different viewpoint:
The evolutionary mechanism of natural selection depends on death, destruction, and violence of the strong against the weak - these things are all perfectly natural, right? On what basis, then, does an atheist judge the natural world to be horribly wrong, unfair, and unjust? The nonbeliever in God doesn't have a good basis for being outraged at injustice, which is their reason for objecting to God in the first place. If you are sure that this natural world is unjust and filled with evil, then you are assuming the reality of some extra-natural (or super-natural) standard by which to make your judgment.