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This question strikes close to my heart. My son left his Christian beliefs and belief in God because he could not balance (correct word?) the facts that God is perfect in mercy and justice.
A response to one of the answers to the question was that we humans do not need to alibi for God's Works. I believe this also.
When we begin to search and try to find human reasons for what Almighty God did and does we are making a mistake. A mistake because it would seem we think that God's actions need to be explained in human terms, finite not infinite.
A favorite verse of mine is Psalm 46:10, it begins, "Be still and know that I am God".