Islamic Scholar, Shaykh Allamah Shibli Nomani
As already related the Prophet (p), when he first settled at Medina, had patched up treaties with the Jews and guaranteed peace and full freedom of life, property and conscience. But when the Quraish wrote to them a threatening and inciting letter, they turned treacherous. The Holy Prophet (p) tried to get the treaty renewed. The Banu Nadir refused and they were banished.
Click to read this, a lot more detailed: Re-Examining Banu Qurayzah Incident
The Banu Quraiza concluded a fresh treaty and they were granted peace. These facts have been narrated briefly in Sahih Muslim in the following words:
‘As reported by Abdullah Ibn Umar, the Jews of the Banu Nadir and the Quraiza fought with the Prophet (p). The Prophet (p) banished the Banu Nadir but allowed the Banu Quraiza to stay on and showed them favours.’
When the Banu Nadir had been banished, their leading chiefs, Huyayy Ibn Akhtab, Abu Rafi and Sallam Ibn Abi al-Huquaiq had migrated to Khaibar and got recognised as leading chiefs. The battle of the Trenches was but the results of their machinations. They travelled far and near agitating the tribes till the whole country rose up in arms and attacked Medina in alliance with the Quraish.
The Jews of the Banu Quraiza had a mind to stick to the treaty, but Huyayy Ibn Akhtab won them over with his guiles, promising to re-establish himself at Medina in case the Quraish abandoned the attack; and this promise he fulfilled.
The Banu Quraiza openly took sides in the battle of the Trenches; and when repulsed, brought the greatest enemy of Islam, Huyayy Ibn Akhtab with them. Now there was no way out for the Prophet (p) but to settle accounts with them once for all.
The battle of the Trenches being over, the Prophet (p) ordered the Muslims not to put off their arms and march against the Quraiza. Had the Quraiza behaved in a spirit of peaceful reconciliation, they should have been surely granted full amnesty after a satisfactory settlement of the issue in hand. But they were determined to resist. They openly abused the Holy Prophet (p) to the face of Ali (ra) who advanced close to their forts leaving the army in the rear.
In short their forts were besieged and the siege continued for a month. In the end they sent word that they would abide by any decision given by Sa’d Ibn Mu’adh. Sa’d Ibn Mu’adh and his tribe (Aus) had been the allies of the Jews, a connection which the Arabs respected more than kinship. The Prophet (p) gave his consent.
The verdict given by Sa’d Ibn Mu’adh, in accordance with instructions of the Torah, was that the militants were to be killed, the women and the children to be made captives and their property to be treated as booty. In Deuteronomy 20:10 we find these orders:
‘When you draw near to a city fight against it, offer terms of peace to it. And if its answer to you is peace and it opens to you, then all the People who are found in it shall do forced labour for you and shall serve you. But if it makes no peace with you.
But makes war against you, then you shall besiege it and when the Lord, your God, gives it into your hands you shall put all its males to the sword, but the women and the little ones, the cattle and everything else in the city, all its spoils, you shall take as booty for yourselves and shall enjoy the spoil of your enemies, which the Lord, your God has given you.’
When Sa’d pronounced the judgement, the Holy Prophet (p) is reported to have said, ‘It is a divine verdict that you have given.’
The words referred to the injunctions quoted above. The words that escaped the lips of the Jews, when the verdict was announced to them also indicate that they as well viewed as one in accordance with the Holy writ.
Huyayy Ibn Akhtab, the perpetrator of all this disturbance, when brought to the place of assassination, looked at the Holy Prophet (p) and uttered these words:
‘I swear by God I am not sorry for having been hostile to three. Ay, the fact is that whosoever forsakes God, God in turn forsakes him.’
Then turning to the people he said
‘O people, we need not worry if we have to obey a divine command. It had been so ordained. It was a punishment for had written down for Israel.’
It should be remembered about Huyayy Ibn Akhtab that, when banished to Khaibar, he had entered into a covenant not to help anyone against the Prophet (p), making God stand witness to it. How he kept this covenant has already been narrated.
Critics have vociferously accused the Muslims of being merciless to the Jews of the Banu Quraiza. But the facts are as follows:
1. On his arrival at Medina, the Holy Prophet (p) entered into a friendly treaty with them, granting them full freedom of conscience and security of life and property.
2. The Banu Quraiza had been inferior in status to the Banu Nadir. If a man from the tribe of the Banu Nadir killed one belonging to the Banu Quraiza, he had to pay only half the blood money. On the other hand if a man from the Banu Quraiza killed one from the Banu Nadir, he had to pay it in full. The Holy Prophet (p) did the Banu Quraiza the favour of allowed them equal status.
3. While banishing the Banu Nadir, the Holy Prophet (p) renewed the treaty with the Banu Quraiza.
4. In spite of all that, the Banu Quraiza violated the treaty and took an active part in the battle of the Trenches.
5. The wives of the Holy Prophet (p) had been lodged in fort for safety. The Quraiza planned to break into the fort.
6. Huyayy Ibn Akhtab, who had been banished for sedition and who had roused the whole Arabia and thus caused the battle of the Trenches, was brought back by the Banu Quraiza, an act that was the prelude to the outbreak of hostilities.
Under the circumstances what better treatment could they deserve?
It has also to be kept in mind that to the Arab an alliance was scared as real kinship. The Banu Quraiza were the allies of the Ansaris. It is why the Ansaris most vehemently pleaded for them. Sa’d Ibn Mu’adh, the chief of the Aus, had in fact been responsible for making the Jews enter into the treaty. He must have been now in a fix; it was the question of life and death for his allies whose caused was forcefully pleaded by all the Ansaris. But what other judgement could Sa’d give.
The number of the killed as given by the historians was 600. But in Sihah (six authentic books of Hadith) the number given is 400. Out of these only one was a woman. She was ordered to be executed as she had killed a Muslim (KHallad) by rolling down a stone from the fort. How bravely she faced death is mentioned in Sunan Abu Dawud.
She knew that she was one of the accused to be executed. One after another they came and were despatched. Each was summoned by name and each time the stunning call fell on her ears. Yet, unaffected she went on conversing with A’isha with frequent bursts of laughter. Suddenly the swordsman cried out her name. With an air of indifference she rose to her feet.
‘Where do you go?’ Asked A’isha. ‘I had committed a crime’, she replied, ‘and now I go to take the penalty’.
With these words she walked off cheerfully and offered her neck to the sword. Whenever A’isha narrated this story she felt struck with wonder. 
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 Sirat -un- Nabi [Sallallahu Alaihi Wasallam] By Shaykh Allamah Shibli Nomani (r.a), volume 2, Page 119 – 124