Tens of Thousands Were Killed in the Civil War against the Tribe of Binyamin (Benjamin). Why?

The background for what the Talmud discusses is in the last few chapters of the Biblical book of (Shoftim) Judges.
Since not everyone is so familiar with the incident, here we will provide a translated version of chapter 20 of (Shoftim) Judges from Sefaria.org. where the civil war is described in detail.

Thereupon all the Israelites—from Dan to Beer-sheba and [from] the land of Gilead—marched forth, and the community assembled as one, before GOD at Mizpah.
All the leaders of the people [and] all the tribes of Israel presented themselves in the assembly of God’s people, 400,000 fighters on foot.—
The Benjaminites heard that the Israelites had come up to Mizpah. —The Israelites said, “Tell us, how did this evil thing happen?”
And that Levite, the husband of the murdered woman, replied, “My concubine and I came to Gibeah of Benjamin to spend the night.
The citizens of Gibeah set out to harm me. They gathered against me around the house in the night; they meant to kill me, and they abused my concubine until she died.
So I took hold of my concubine and I cut her in pieces and sent them through every part of Israel’s territory. For an outrageous act of depravity had been committed in Israel.
Now you are all Israelites; produce a plan of action here and now!”
Then all the people rose as one and declared, “We will not go back to our homes, we will not enter our houses!
But this is what we will do to Gibeah: [we will wage war] against it according to lot.
We will take from all the tribes of Israel ten of every hundred, a hundred of every thousand, and a thousand of every ten thousand to supply provisions for the troops—to prepare for their going to Geba in Benjamin for all the outrage it has committed in Israel.”
So Israel’s entire force, united as one, massed against the town.
And the tribes of Israel sent agents through the whole tribe of Benjamin, saying, “What is this evil thing that has happened among you?
Come, hand over those scoundrels in Gibeah so that we may put them to death and stamp out the evil from Israel.” But the Benjaminites would not yield to the demand of their fellow Israelites.
So the Benjaminites gathered from their towns to Gibeah in order to take the field against the Israelites.
On that day the Benjaminites mustered from the towns 26,000 fighters, mustered apart from the inhabitants of Gibeah; 700 elite troops
of these forces—700 of the best troops—were left-handed. Every one of them could sling a stone at a hair and not miss.
Those on Israel’s side—other than Benjamin—mustered 400,000 fighters, every one of them a warrior.
They proceeded to Bethel and inquired of God; the Israelites asked, “Who of us shall advance first to fight the Benjaminites?” And GOD replied, “Judah first.”
So the Israelites arose in the morning and encamped against Gibeah.
Israel’s side took the field against the Benjaminites; those on Israel’s side drew up in battle order against them at Gibeah.
But the Benjaminites issued from Gibeah, and that day they struck down 22,000 of the Israelites.
Now the army—Israel’s side—rallied and again drew up in battle order at the same place as they had on the first day.
For the Israelites had gone up and wept before GOD until evening. They had inquired of GOD, “Shall we again join battle with our kinsmen the Benjaminites?” And GOD had replied, “March against them.”
The Israelites advanced against the Benjaminites on the second day.
But the Benjaminites came out from Gibeah against them on the second day and struck down 18,000 more of the Israelites, all of them fighters.
Then all the Israelites, all the army, went up and came to Bethel and they sat there, weeping before GOD. They fasted that day until evening, and presented burnt offerings and offerings of well-being to GOD.
The Israelites inquired of GOD (for the Ark of God’s Covenant was there in those days,
and Phinehas son of Eleazar son of Aaron the priest ministered before [God] in those days), “Shall we again take the field against our kinsmen the Benjaminites, or shall we not?” GOD answered, “Go up, for tomorrow I will deliver them into your hands.”
Israel set up ambushes against Gibeah on all sides.
And on the third day, the Israelites went up against the Benjaminites, as before, and engaged them in battle at Gibeah.
The Benjaminites dashed out to meet the army and were drawn away from the town onto the roads, of which one runs to Bethel and the other to Gibeah. As before, they started out by striking some of the troops dead in the open field, about 30 of the Israelites.
The Benjaminites thought, “They are being routed before us as previously.” But the Israelites had planned: “We will take to flight and draw them away from the town to the roads.”
And while everyone else on Israel’s side had moved away from their positions and had drawn up in battle order at Baal-tamar, the Israelite ambush was rushing out from its position at Maareh-geba.
Thus 10,000 of the best troops from all Israel came to a point south of Gibeah, and the battle was furious. Before they realized that disaster was approaching,
GOD routed the Benjaminites before Israel. That day the Israelites slew 25,100 of the Benjaminites, all of them fighters.
Then the Benjaminites realized that they were routed. Now the rest of Israel’s side had yielded ground to the Benjaminites, for they relied on the ambush that they had laid against Gibeah.
One ambush quickly deployed against Gibeah, and the other ambush advanced and put the whole town to the sword.
A time had been agreed upon by the rest of Israel’s side with those in ambush: When a huge column of smoke was sent up from the town,
the rest of Israel’s side was to turn about in battle. Benjamin had begun by striking dead about 30 men on Israel’s side, and they thought, “They are being routed before us as in the previous fighting.”
But when the column, the pillar of smoke, began to rise from the city, the Benjaminites looked behind them, and there was the whole town going up in smoke to the sky!
And now Israel’s side turned about, and Benjamin’s side was thrown into panic, for they realized that disaster had overtaken them.
They retreated before Israel’s force along the road to the wilderness, where the fighting caught up with them; meanwhile those from the towns were massacring them in it.
They encircled the Benjaminites, pursued them, and trod them down [from] Menuhah to a point opposite Gibeah on the east.
That day 18,000 of the Benjaminites fell, all of them brave men.
They turned and fled to the wilderness, to the Rock of Rimmon; but [the Israelites] picked off another 5,000 on the roads and, continuing in hot pursuit of them up to Gidom, they slew 2,000 more.
Thus the Benjaminite fighters who fell that day numbered 25,000, all of them brave men.
But 600 others turned and fled to the wilderness, to the Rock of Rimmon; they remained at the Rock of Rimmon four months.
Those on Israel’s side, meanwhile, turned back to the rest of the Benjaminites and put them to the sword—towns, people, cattle—everything that remained. Finally, they set fire to all the towns that were left.

The Talmud Sanhedrin 103b as translated and explained by Sefaria.org provides the reason for the loss of tens of thousands in the Tribal Civil War:

It is taught in a baraita that Rabbi Natan says: The distance from Gerav, where Micah resided, to Shiloh, where the Tabernacle was at that time, was three mil, and the smoke from the arrangement of wood on the altar in Shiloh and the smoke from the worship of the idol of Micah would intermingle with each other.
The ministering angels sought to dismiss him from the world. The Holy One, Blessed be He, said to them: Leave him, as his bread is available for travelers. And it is for this matter, the sin of Micah’s idol, that the people involved in the incident of the concubine in Gibeah were punished. The tribes of Israel waged war with the tribe of Benjamin and forty thousand of them were killed (Rashi). The Holy One, Blessed be He, said to them: You did not protest for My honor and took no action to destroy Micah’s idol, but you protested for the honor of one of flesh and blood.

Rabbi Avraham the son of Rambam sums up the Talmud’s analysis of the incident with a slight change of wording.

Rabbi Avraham was asked (שו”ת רבי אברהם בן הרמב”ם סימן לא)

What is the reason that the men of Givah (Gibeah) won after the big abomination came out from them?

Rabbi Avraham answered the victory of the men of Givah (Gibeah) against Israel was a punishment for Israel on account of an abundance of foreign worship (idolatry) as our sages stated, “for the concubine of Givah (Gibeah) you were zealous; for my great name in Dan you were not zealous”. And the fact that he (G-d told them through the Urim V’tumim) “go up against them”, it did not imply they would win. And we have a received tradition that  after they fought the sons of Dan and blotted out the memory of the idol of Micah and fasted, cried, and repented, then were they guaranteed (by Hashem) a victory which was fulfilled afterwards.

Rashi and Radak Disagree with the View that the Idol of Micah was Eradicated During the Time of the Tribal Civil War.

Rashi to (Shoftim) Judges  18:30 believes the idol lasted until the time of Sancheriv. Radak to (Shoftim) Judges  18:30 believes the idol lasted until the ark went into exile and Shiloh stopped being the place of the Tabernacle. It appears that according to Rashi and Radak after the tribes of Israel lost two times, Hashem allowed the tribes to win the civil war without full repentance.

At the time of the Tribal Civil War the holiest site in Judaism was at Shiloh. In our times the holiest site in Judaism is located at the Temple Mount in Jerusalem. With this in mind  it is our hope that the reader will become more sensitive towards the spiritual problem and dangers of having mosques on the Temple Mount.

Please read the following posts for a better understanding why those mosques present such a problem.