Women and Children were usually not killed but taken as slaves, women usually ended up as concubines (slaves used for sexual activity),
Sura 70:22-30; 23:5-6; 4:24 give full permission for the Muslims to rape their female slaves (the girls taken in war). In Sura 33:50 a special permission is given for Muhammed.
"...who restrain their carnal desires (except with their wives and slave girls, for these are lawful to them..." (Sura 23: 5-6)
"And all married women are forbidden unto you save those captives whom your right hand possess. It is a decree of Allah for you (Sura 4: 24).
According to Tabari vol.39, p.194 the ruler of Alexandria gave a young Christian girl as a gift to Muhammad, her name was Mariyam. Muhammad never married her but used to sleep with her, and she even gave birth to a son who died after 18 months..
According to Sahih Bukhari vol.5#637 Ali had sex with a slave girl whom he saw and found beautiful, and Muhammad seemed to have no objections.
Narrated Buraida:
The prophet sent Ali to Khalid to bring the Khumus (part of the war booty) and I hated Ali, and Ali had taken a bath (after a sexual act with a slave girl from the Khumus). I said to Khalid, "Don't you see this (i.e. Ali)? When we reached the prophet I mentioned that to him. He said, "O Buraida! Do you hate Ali?" I said, "Yes." He said, "Do you hate him for he deserves more than that from the Khumus." (Sahih Bukhari, vol.5, #637)
some were even raped on the battle field:
According to Sahih Bukhari vol.9#506; Sahih Muslim vol.2#3371 Muhammad’s followers used to come to Muhammad after battles, to seek permission and advise to engage in sexual activity with the girls taken in battle. They doubted for several reasons, however, permission was granted.
At one point Muhammad gave them permission and told them that it is up to Allah who gets created anyway, thus permission was given.
a. The permission from the Koran
"Prophet, We have made lawful to you the wives whom you have granted dowries and the slave girls whom God has given you as booty;..." (Sura 33: 50)
b. Doubt due to fear of less money for selling pregnant slaves
Narrated Abu Said Al-Khudri that while he was sitting with Allah's messenger we said, "Oh Allah's messenger, we got female captives as our booty, and we are interested in their prices, what is your opinion about coitus interruptus?" The prophet said, "Do you really do that? It is better for you not to do it. No soul that which Allah has destined to exist, but will surely come into existence." (Sahih Bukhari, vol.3, # 432) (further reference Bukhari Vol. 3, #718)
c. Fear due to pregnancy
Narrated Abu Said Al-Khudri that during the battle with Bani Al-Mustaliq they (Muslims) captured some females and intended to have sexual relations with them without impregnating them. So they asked the prophet about coitus interruptus. The prophet said, "It is better that you should not do it, for Allah has written whom He is going to create till the Day of Resurrection". (Sahih Bukhari, vol.9, #506) (further reference Bukhari 5: 459)
d. Lust or ransom?
Abu Sirma said to Abu Said al Khudri: "O Abu Said, did you hear Allah's messenger mentioning about al-azl (coitus interrupts)?" He said, "Yes", and added: "We went out with Allah's messenger on the expedition to the Mustaliq and took captive some excellent Arab women; and we desired them for we were suffering from the absence of our wives, (but at the same time) we also desired ransom for them. So we decided to have sexual intercourse with them but by observing azl" (withdrawing the male sexual organ before emission of semen to avoid conception). But we said: "We are doing an act whereas Allah's messenger is amongst us; why not ask him?" So we asked Allah's messenger and he said: "It does not matter if you do not do it, for every soul that is to be born up to the Day of Resurrection will be born". (Sahih Muslim vol.2, # 3371)
e. Doubt since their men are polytheists
Abu Said al-Khudri reported that at the Battle of Hunain Allah's messenger sent an army to Autas and encountered the enemy and fought with them. Having overcome them and taken them captives, the Companions of Allah's messenger seemed to refrain from having intercourse with captive women because of their husbands being polytheists. Then Allah, Most High, sent down regarding that: "And women already married, except those whom your right hands possess (Quran - 4:24), (i.e. they were lawful for them when their Idda (menstrual) period came to and end). (Sahih Muslim, vol.2, #3432)
f. Doubt since their husbands watch them being raped
Abu Said al-Khudri said: "The apostle of Allah sent a military expedition to Awtas on the occasion of the battle of Hunain. They met their enemy and fought with them. They defeated them and took them captives. Some of the Companions of the apostle of Allah were reluctant to have intercourse with the female captives in the presence of their husbands who were unbelievers. So Allah, the Exalted, sent down the Quranic verse, "And all married women (are forbidden) unto your save those (captives) whom your right hand possesses". That is to say, they are lawful for them when they complete their waiting period."" [The Quran verse is 4:24]. (Sunan of Abu Dawud, vol.2, #2150)
In Some cases night raids were made, and there was the great possibility that women and children could be killed, however, here we see the real nature of Islam when it considers the non-believer:
Sahih Muslim, Book 019, Number 4321:
It is reported on the authority of Sa'b b. Jaththama that the Prophet of Allah (may peace be upon him), when asked about the women and children of the polytheists being killed during the night raid, said: They are from them.
Obviously, in attacking and invading territory, children and women were spared not so much because of their value, but because of their potentiality as slaves.
If However, such were killed, well then…they are from them (the non-believers)
This becomes obvious from Islamic ideology which states that the blood of a Muslim has higher value than that of a non-Muslim; in other words, in case of murder a Muslim cannot be punished for the murder of a Christian (Ibn Hazm, vol.8, p.39).
Muhammad even promised his companions paradise as a definite reward if they engaged in these battle
Sahih Muslim, Book 020, Number 4681:
The tradition has been narrated on the authority of 'Abdullah b. Qais. He heard it from his father who, while facing the enemy, reported that the Messenger of Allah (may peace be upon him) said: Surely, the gates of Paradise are under the shadows of the swords. A man in a shabby condition got up and said; Abu Musa, did you hear the Messenger of Allah (may peace be upon him) say this? He said: Yes. (The narrator said): He returned to his friends and said: I greet you (a farewell greeting). Then he broke the sheath of his sword, threw it away, advanced with his (naked) sword towards the enemy and fought (them) with it until he was slain.
Bukhari, 4.266A:
Narrated Salim Abu An-Nadr:
(the freed slave of 'Umar bin 'Ubaidullah) I was Umar's clerk. Once Abdullah bin Abi Aufa wrote a letter to 'Umar when he proceeded to Al-Haruriya. I read in it that Allah's Apostle in one of his military expeditions against the enemy, waited till the sun declined and then he got up amongst the people saying O people! Do not wish to meet the enemy, and ask Allah for safety, but when you face the enemy, be patient, and remember that Paradise is under the shades of swords." Then he said, "O Allah, the Revealer of the Holy Book, and the Mover of the clouds and the Defeater of the clans, defeat them, and grant us victory over them."
Muhammad even warned his followers that those who refrained from fighting the non-believers would die as hypocrites:
Abu Dawud, Book 14, Number 2496:
Abu Hurairah reported the Prophet as saying:
He who dies without having fought or having felt fighting (against the infidels) to be his duty will die guilty of a kind of hypocrisy”.
Even Further we have the killing of apostates, those who leave Islam, and there is no mercy shown.
According to Bukhari, vol. 9, #64 apostates are to be killed wherever they are found:
"So, wherever you find them, kill them, for whoever kills them shall have reward on the Day of Resurrection."
A incident narrated by Ikrima, Bukhari vol. 9 #57 reveals this even further:
"Narrated Ikrima: "Some atheists were brought to Ali [Muhammad's son in law, the fourth Caliph] and he burnt them [to death]. The news of this event reached Ibn Abbas who said, 'If I had been in his place, I would not have burnt them as Allah's messenger forbade it saying "Do not punish anybody with Allah's punishment (fire)." I would have killed them according to the statement of Allah's messenger 'Whoever changed his Islamic religion, then kill him''".