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The 42 boys were sinners, and God has the right to punish sinners with death. Those who say that this seems unnecessarily cruel or unfair do not have a proper view of the seriousness of sin.
Some argue that it was immoral and unfair for God to kill forty-two boys for mocking Elisha. Here is the relevant passage:
2 Kings 2:23-24- 23 He went up from there to Bethel, and while he was going up on the way, some small boys came out of the city and jeered at him, saying, “Go up, you baldhead! Go up, you baldhead!” 24 And he turned around, and when he saw them, he cursed them in the name of the Lord. And two she-bears came out of the woods and tore forty-two of the boys.
If you content that it was unfair for God to punish the forty-two boys with death, then we must ask, "What moral standard are you using to judge that God was unfair or immoral to do this?"
More than likely, you simply cannot point to any moral standard that judges God to be wrong to do this. And, if you use the Bible's moral standard, then:
The Bible teaches that evil and sin deserve the punishment of death and hell. The forty-two boys sinned by mocking God's prophet. God does not always punish sin with death immediately, but He sometimes does, and He did so in this instance. The boys fully deserved their punishment, and God was not wrong to punish them. He was simply doing what His own moral law demands.
If you have an emotional problem with God's action in 2 Kings 2:23-24
Everyone who has not been saved through faith in Jesus deserves the exact same punishment as what the forty-two boys received.
Some people have trouble accepting possible explanations to alleged contradictions in the Bible, especially ones that they consider a stretch. For example, Dan Barker, president of the Freedom From Religion Foundation, says this:
I have received numerous replies from Christians who think that these contradictions are either trivial or easily explained. Yet not a single "explanation" has been convincing.
The fact is that there are plausible explanations for every alleged contradiction in the Bible. That there is a plausible explanation for an alleged contradiction does not mean that it is definitely the correct explanation for the alleged contradiction.
However, as long as a possible explanation has been suggested, then it has been objectively demonstrated that there is no necessary contradiction regarding the Bible verses and passages brought up.
When people like Dan Barker say that they don't find a particular explanation for a contradiction "convincing," then that is merely their opinion. A plausible explanation has been suggested that eliminates the necessary alleged contradiction. They simply don't like it, which is not at all a relevant argument against the explanation.
To read more about solutions to Bible contradictions and difficulties, check out Norman Geisler's The Big Book of Bible Difficulties: Clear and Concise Answers from Genesis to Revelation. While we do not agree with some of Geisler's theology, particularly concerning his view of predestination, this book is still an excellent resource. It is thorough and filled with research.
Another book to check out is Tim Chaffey's Demolishing Supposed Bible Contradictions: Exploring Forty Alleged Contraditions, which also answers many alleged contradictions in the Bible.