Explaining the sovereignty of God to an atheist is frustratingly difficult. The Old Testament contains some very difficult descriptions of God's judgement, some of which are against whole nations. In the atheist's mind, this is comparable to genocidal dictators killing in the name of their ideologies.
But not all rules apply to all people. Authority can vary from person to person. For example, I originally wrote this article from my bedroom using my smart phone. The key word there is "my". I have full authority to enter this house, or use that phone (or the laptop upon which I am currently re-writing this article). If I should lose my key, I could rightfully pick the lock to my house. However, if you tried to pick my lock, I could have you arrested for it. I could hack my phone if I forget my passcode, but you would also be arrested for that. A police officer can force you to go to a temporary holding cell, but it would be considered false imprisonment if I attempted to do so.
As you can see, authority varies according to ownership and rank. Here's the catch: God owns everything and outranks everyone. Even you are His creation, living by His power and grace in His universe. Therefore, while it would be genocide for a dictator to kill an entire people group, God has the right to do so. In fact, the only reason it's ever wrong to kill a human being at all is because it's not our right to do so. It's like picking God's locks. Therefore, we have no right to tell God He is evil for how He judges sin.
But what we can do is praise Him for how He ultimately chose to. See, while many sinners receive His wrath, God has actually provided a very gracious way for them to avoid it. Everyone who repents of their sin and confesses Jesus as the risen Lord will receive an eternal inheritance in God's Kingdom, a place where the locks are unpickable! Therefore, rather than complain that God judges sin, repent of it, and share in His Son's reward!