Welcome to the boards, WDIK :)
To come to an answer to your question, where you really have to start is the fact that all men, without exception, are sincerely evil. How is it that God would allow entire villages to be wiped out? It wasn't because He is cruel, but because He is just.
Let me give you a few verses to help you see. It's worth it to meditate on every tiny clause within this passage, because each one speaks volumes about man.
Romans 3:9-18
For we have already charged that all, both Jews and Greeks, are under sin, 10as it is written:
"None is righteous, no, not one;
11 no one understands;
no one seeks for God.
12 All have turned aside; together they have become worthless;
no one does good,
not even one."
13 "Their throat is an open grave;
they use their tongues to deceive."
"The venom of asps is under their lips."
14 "Their mouth is full of curses and bitterness."
15 "Their feet are swift to shed blood;
16 in their paths are ruin and misery,
17 and the way of peace they have not known."
18 "There is no fear of God before their eyes."
From the very first two people who ever walked the earth, down to the most recently-born child in the world, this passage is talking about each and every one of them. You notice that the author of this passage is careful to let his recipients understand that these charges include absolutely everybody, without exception: Those destroyed in Sodom and Gamorrah, the Moabites who were destroyed, even their children, and even you.
Genesis 6:5 - The LORD saw that the wickedness of man was great in the earth, and that every intention of the thoughts of his heart was only evil continually.
Man is capable of a supreme level of wickedness. If you pay attention to this verse, it is essentially saying that the thoughts of all people on the earth, with very very few excepted, were only one wicked, vile thought after another.
Jeremiah 17:9 - The heart is deceitful above all things, and desperately sick; who can understand it?
We often talk of "following your heart" so as to learn something, but the truth is that the heart of man is gravely wicked, and relishes in deceit. The heart lies to us about others, about ourselves, and about God. What we feel and believe, what comes from the heart, from our inmost being, lies about the truth. The ninth commandment is "you shall not bear false witness," though because of our sin nature, the heart bears a false witness all the time.
Isaiah 64:6 - We have all become like one who is unclean, and all our righteous deeds are like a polluted garment. We all fade like a leaf, and our iniquities, like the wind, take us away.
Most of the time we make an appeal to the good things we've done so as to not say that we are a bad person, and that our conduct would pass the bar before God. However, God states that even our righteousness is like a polluted garment. I don't say this for crudeness sake, but this will probably guide your understanding to the force of this passage, the original meaning of that phrase is menstrual clothing. It's of no effect to really say something is dirty, but when you try and offer a righteousness before your God, this is the essence of what you are offering him; something repulsive and demeaning to Him.
All of these considered, it is not out of cruelty that God has allowed people to be wiped out, or has done it by His own hand; in fact, Scripturally speaking, it is a fair execution of justice, in the same way a murderer is brought to the scaffold. When you account for the multitude of sins that one man will commit over his life, then you consider the sins that an entire city will commit, or even a nation, can you see this accumulating to incur God's anger? Here is man living in complete and total defiance of God, even a city of people doing the same, and it is that God has been patient not to destroy them, but has been quite merciful.
If you still have doubts about it, consider the most wicked men in the world, and what they have been capable of. It's a very good living picture of what man likes to do with sin. This is the way man naturally likes to go. Even though it is in perfect rebellion against God, He loves it. But even then, consider the thoughts that have gone through your own mind, even in the past day. What are those thoughts like, when laid against the moral compass?
But then the next thing to consider is that God is a holy God. Perhaps you have come across this, but the Hebrew language has a particular way of emphasizing something, and that is by repeating it. The angels, when they sing in heaven, they sing, "Holy, holy, holy is the Lord God Almighty." Usually a Jew would only emphasize this trait twice, but this one is stated three times.
Isaiah 6:3 - "Holy, holy, holy is the Lord of hosts!"
Revelation 4:8 - "Holy holy holy is the Lord God Almighty, who was and is and is to come."
Holiness in part means righteousness and purity, but it also means that God is distinct. He is different from everything else. Whosoever tries to approach Him, must approach Him on His terms, much the same way that not anyone could approach a king, and thus not just anyone could approach God. Only that which is perfect and pure and without blemish could possibly approach God. How is it that an entire city or nation of people can expect to intrude on His presence with their great compilation of sin going before them and following after them?
I hope I haven't given you too much in this, though these are verses worth meditating on, and considering them not only in the light of the people and nations in the Bible, but yourself as well. This is the essential and basic condition of man.
I hope that this has profited you, and that God will use it to draw you to Himself. Please don't leave this thread to sink and go unanswered. Stick with us, and let us help you however we can.
God bless,
Jake