Now, while I don't think that chapter 20 is quite as shocking in a simple sense (I mean after all, this isn't so personal; it's war, and this is just the way war is.) there is something more troubling about it from the point of view of an apologist: While God is completely absent from the previous chapter, it appears that the civil war that unfolds in response to the events of chapter 19 is undertaken with the express blessing of God. This is pretty much genocide we're about to see here, and what's more, genocide against the Israelites' own brothers.
I will, of course, offer a possible explanation of the apparent actions of God in this chapter, but I honestly have to admit that I'm grasping at straws here, and even my stretching of the interpretation of this chapter doesn't come across very pleasant at all. The easiest way out would be to say that when "the LORD said" in this chapter, it's not God, but the priests speaking falsely as though on behalf of God or some such thing. (Note that in verse 9, they say they "will go up by lot", raising the possibility that they essentially drew straws and considered the result to be the will of God.) Such an interpretation may create more problems than it solves for the apologist. I mention it only as a temptation, not as something I consider to be a reasonable response.
So here's the recap: Fighting men from all the tribes of Israel except for Benjamin (and probably Levi) gather together in Mizpeh to meet the Levite from chapter 19 and hear his story. Now the story he tells is technically true, but he leaves out the parts about his concubine being unfaithful to him and how he and his host actually gave the concubine to the crowd willingly. It's possible that the actual words of his story supply more detail than we read here, but it does sound like he's leaving out any details that paint him in bad light, which one would expect. The men of Israel vow that they will not return home until the rapists are brought to justice, and so they go to war.
The whole text of the battle that ensues is marked repeatedly by the SAB as absurd, violent and unjust. While I and any rational person would agree that this is a violent story, I don't see anything absurd about it, other than the fact that it's blown way out of proportion, which leads me to somewhat agree with the injustice label. I say "somewhat" because I suspect if this had not been an all-out war and only the men of Gibeah had been slaughtered, the label would still be there in the SAB, but I think I and many others would feel it was quite just. That being said, the fact that their fellow Benjamites are protecting them from justice may make them fair game, but that's more of a grey area in my mind.
The men of Benjamin fight exceptionally well, killing somewhere around 40,000 Israelites before finally losing. A note of accuracy that does little to soften the atrocity of the moment should be inserted here in response to the notes of the SAB. Verse 44 notes "Another 25,000 Benjamites are killed..." Actually, these are the same ones. If you read the story carefully, you'll note that the Benjamites started out with 26,000 soldiers (v. 15), so killing 50,000 of them would have to be an error. It isn't though; verse 35 is a summary of the battle while the following verses are a telling of the details of that battle, and a breakdown of how and where the Benjamites were defeated. In addition to the killing of soldiers, at the beginning of the final battle, they burn down the city of Gibeah, and after the battle, they pretty much just go nuts and destroy every city in the tribe of Benjamin.
Okay, so let me get down to it: this is horrible. It's a horrific, shameful moment in the history of Israel, and in addition to that, it appears that God is actually involved this time. What can you say? There are actually a few possibilities. One, which I've already hinted at, is that God approves. That is to say--and the distinction is important--that God approves of taking justice against Benjamin for allowing such an evil thing to happen in their midst. It does not necessarily mean that God approves of the all-out genocide and large-scale destruction that ensues after the battle. I can just barely believe of God that He might want not just the men of Gibeah destroyed, but the soldiers who fought to protect them. I don't believe that God intended the entire tribe to be decimated, no matter what, and I don't think the text supports that.
Another possibility that makes perhaps a bit more sense (although doesn't make things look much better) is that God led the men of Israel to do this thing as a form of punishment on them as well as on Benjamin. It hearkens back to Egypt and how once Pharaoh decided he would not let the Israelites go no matter what, God caused him to be hardened in his heart and stick to his guns even to the point of his own ruin. The men of Israel were so dead set on exacting revenge, and were so deeply steeped in sin themselves (if the rest of the book of Judges is any indication) that God said, "Sure! Go ahead and attack! Everyone is going to get exactly what they deserve..." Some people refuse to have faith in the God of the Bible because they pray, and do not get what they ask for, but Psalm 106:15 talks of what may be at times the worst curse that God can ever give someone: "He gave them their request".