Deuteronomy has plenty off of verses in regards to this off the top of my head. Here's one example from a simple google search.
http://www.allaboutgod.com/truth/deuteronomy-20.htm
God himself ordering tand ordaining the complete genocide, pillaging, and yes, raping unless you happen to be one of those types that believes women to be property and having no rights, literally litters the bible. Everything following egypt is chock full of it. What bible are you reading?
You are both getting confused here because you don't understand the context of what is going on.
WHY FIGHT THESE NATIONS?
God tells Moses the reason he was using them as a nation to fight these specific nations In Deut 9:4
4 “Do not say in your heart when God drives them away from before you, ‘It was because of my own righteousness that God has brought me in to take possession of this land.’ Rather, it is because of the wickedness of these nations that God is driving them away from before you. 5 It is not because of your righteousness or the uprightness of your heart that you are going in to take possession of their land. Instead, it is because of the wickedness of these nations that Jehovah your God is driving them away from before you and in order to carry out the word that God swore to your forefathers, Abraham, Isaac, and Jacob. "
The nations are wicked engaging in child sacrifice, beast and child prostitution and god deems they gots to go. Plus many of them attacked Israel when they were leaving Egypt and in a weakened condition and because they didn't help them they in turn would receive no help.
RULES OF CONDUCT
That said he outlines the rules of engaging in combat with these nations:
Deut 7:1-3
"When the LORD your God brings you into the land you are about to enter and occupy, he will clear away many nations ahead of you: the Hittites, Girgashites, Amorites, Canaanites, Perizzites, Hivites, and Jebusites. These seven nations are greater and more numerous than you.
2: You must completely destroy them. Make no treaties with them and show them no mercy.
3: You must not intermarry with them. Do not let your daughters and sons marry their sons and daughters,
The rules continue as you noted in Deuteronomy 20:10-14 but that deals with a nation that surrenders. If they surrender they men were put to forced labor and the women and children sparred.
BUT HOW DO WE KNOW THEY WEREN'T RAPING THE WOMEN?
During the military campaign the only way the war could be holy was by them never engaging in any 'unclean' practice. This included not only sex but a orgasm of any kind:
Deut 23:9-10
When you are encamped against your enemies, keep away from everything impure. If one of your men is unclean because of a nocturnal emission, he is to go outside the camp and stay there.
Therefore sexual contact with women, even their own wives, was prohibited to them and they voluntarily abstained from it. This was why Uriah who was interesting enough a Hittite, when called in from the field by King David, did not go at night to his home in Jerusalem to be with his wife. When King David, ignoring the sacred requirements of the military campaign, asked Uriah why he had not gone home that night, that loyal soldier replied: “The ark, and Israel, and Judah, abide in booths; and my lord Joab, and the servants of my lord, are encamped in the open field; shall I then go into my house, to eat and to drink, and to lie with my wife? as thou livest, and as thy soul liveth, I will not do this thing.”
Also god outlined what was to be done with women that were brought back to Israel from one of the foreign nations:
Deut 21:10-12
When you go to war against your enemies and the LORD your God delivers them into your hands and you take captives, Bring her into your home and have her shave her head, trim her nails, and put aside the clothes she was wearing when captured. After she has lived in your house and mourned her father and mother for a full month, then you may go to her and be her husband and she shall be your wife. If you are not pleased with her, let her go wherever she wishes. You must not sell her or treat her as a slave, since you have dishonored her.
So no raping no dealing with them in any violent way. If they did try and Rape someone Deut 22:25 tells us what would happen:
But if out in the country a man happens to meet a young woman pledged to be married and rapes her, only the man who has done this shall die. Do nothing to the woman; she has committed no sin deserving death. This case is like that of someone who attacks and murders a neighbor.
You rape someone you die. The one time a women is raped in the bible it is so appalling to the rest of the nation that they go to war with the family line that was responsible and almost wipe every single one out.
Plus its not a situation where the bible is just being vague and doesn't acknowledge rape. God tells the Israelites that if they don't worship him and instead worship gods of the other nations and commit child sacrafice that he will not protect them when they go to war and there will be a profound difference between their warfare when god is with them and when he is not. He describes what would happen in Isa 13:
Isa 13:16
Their little children will be dashed to death before their eyes. Their homes will be sacked, and their wives will be raped.
So no raping under any circumstances.
Further the Israelites also had strict guidelines with their slaves. They could not harm them in any way nor push them to do any task they weren't willing to do themselves. On top of that they were only slaves for 7 years at which point they were to be released. Evidence that they were not dealt harshly had to do with the law that forbid it but also that many of the nations that surrendered became prominent individuals within the Isrealite court system.
I hope that helps