The spiritual reason Numbers 31 contains literal atrocities

People will certainly ask you about problematic passages in the Word of God in the literal sense. It matters so much to have answers ready for those difficult questions that are actually loving and healthy. 

1 Peter 3:15 King James Version

15 But sanctify the Lord God in your hearts: and be ready always to give an answer to every man that asketh you a reason of the hope that is in you with meekness and fear:

One wishes in this spirit to "give an answer" to the problematic parts of Numbers 31 involving the slaughter of all the men, all the male children, and all the women who are not virgins. Whatever this slaughter was for the children of Israel, for all of humanity in all times and places this slaughter represents purification from sin and error.

Men, women, sons, daughters, all of these express goods and truths or evils and falsehoods in various relations to each other. The clue that this chapter is about purification can be seen quite clearly in verses 23 and 24, where it talks of passing everything through the fire except that which should rather be passed through the water. 

It says this about fire and water because it is by a trial by fire, temptation of the heart, that we are purified of sin; and by a trial by water, temptation of the thoughts, that we are purified of error. Remember, this is the Lord who tries the heart and reins (kidneys, which process water, which means purifying thought). 

This is the Lord who brings us through fire and water to a wealthy place (Psalms 66:12, other places).

Now here is a brief and summary key of the chapter in question courtesy of New Christian Bible Study, but it was appropriate to give the former first:

"Verses 1-12. Concerning the removal of falsifications of truth with the man of the Spiritual Church by victory in temptation.

Verses 13-24. That purification must follow, because the outward rejection of falsified truths must be succeeded by the separation of impure affections, and incipient falsities, as well as of whatever impurities yet adhere externally to the acquired goods and truths of the church.

Verses 25-31. Concerning the new quality by victory, and the clear distinction to be made between the Celestial and Spiritual, or between good and truth.

Verses 32-54. That goods and truths of every kind and degree, in this new state, are fully ascribed to the Lord". 

Psalms 66:12 - King James Version (KJV)

<12> Thou hast caused men to ride over our heads; we went through fire and through water: but thou broughtest us out into a wealthy place.

We see a similar problematic statement about killing infants in Psalm 137:9, where someone is called "blessed" for dashing Babylonian children on the stones! But this too must be understood for what it really is: Blessed is someone who destroys within themselves and others the falsehoods and profanations that come from Babylon, which are its children, by dashing these evils and falsehoods against the stones of divine truth. All the problematic passages in the Word resolve into meanings like this; because the Lord uses violent language to communicate peaceful points, just as Mom tells her kids to come down to dinner this instant or she will 'skin them alive'.

Psalms 137:9 - King James Version (KJV)

<9> Happy shall he be, that taketh and dasheth thy little ones against the stones.

One takes this opportunity to share one of the fruits of studying the Writings of the Latin Word alongside the Hebrew and Greek Testaments:  the Old Testament becomes more like an old friend and less like a scary monster.