Peace or Jihad? Abrogation in Islam
David Bukay in the Middle East Quarterly presents a comprehensive overview of the all-important concept of abrogation in Islam: the principle by which many Islamic exegetes hold that the violent passages of the Qur'an take precedence over the peaceful ones.

How does the theological debate over abrogation impact contemporary policy formulation? While not all terrorism is rooted in Islam, the religion is an enabler for many. It is wrong to assume that more extreme interpretations of religion are illegitimate. Statements that there is no compulsion in religion and that jihad is primarily about internal struggle and not about holy war may receive applause in university lecture halls and diplomatic board rooms, but they misunderstand the importance of abrogation in Islamic theology. It is important to acknowledge that what university scholars believe, and what most Muslims—or more extreme Muslims—believe are two different things. For many Islamists and radical Muslims, abrogation is real and what the West calls terror is, indeed, just.

During the lifetime of Muhammad, the Islamic community passed through three stages. In the beginning from 610 until 622, God commanded restraint. As the Muslims relocated to Medina (623-26), God permitted Muslims only to fight in a defensive war. However, in the last six years of Muhammad's life (626-32), God permitted Muslims to fight an aggressive war first against polytheists,[52] and later against monotheists like the Jews of Khaybar.[53] Once Muhammad was given permission to kill in the name of God, he instigated battle.

Chapter 9 of the Qur'an, in English called "Ultimatum," is the most important concerning the issues of abrogation and jihad against unbelievers. It is the only chapter that does not begin "in the name of God, most benevolent, ever-merciful."[54] Commentators agree that Muhammad received this revelation in 631, the year before his death, when he had returned to Mecca and was at his strongest.[55] Muhammad bin Ismail al-Bukhari (810-70), compiler of one of the most authoritative collections of the hadith, said that "Ultimatum" was the last chapter revealed to Muhammad[56] although others suggest it might have been penultimate. Regardless, coming at or near the very end of Muhammad's life, "Ultimatum" trumps earlier revelations.

Because this chapter contains violent passages, it abrogates previous peaceful content. Muhsin Khan, the translator of Sahih al-Bukhari, says God revealed "Ultimatum" in order to discard restraint and to command Muslims to fight against all the pagans as well as against the People of the Book if they do not embrace Islam or until they pay religious taxes. So, at first aggressive fighting was forbidden; it later became permissible (2:190) and subsequently obligatory (9:5).[57] This "verse of the sword" abrogated, canceled, and replaced 124 verses that called for tolerance, compassion, and peace.[58]

Suyuti said that everything in the Qur'an about forgiveness and peace is abrogated by verse 9:5, which orders Muslims to fight the unbelievers and to establish God's kingdom on earth.

Prior to receiving "Ultimatum," Muhammad had reached agreements with various Arab tribes. But when God gave Muhammad a revelation (2:190-2), Muhammad felt justified in breaking his cease-fire. For Isma'il bin Kathir (1301-73), a student of Ibn Taymiyya and an influential Qur'an interpreter in his own right, it is clear: As jihad involves death and the killing of men, God draws attention to the fact that disbelief, polytheism, and avoidance of God's path as shown by the Qur'an are worse than killing them.[59] This creates license for future generations of Muslims to kill non-Muslims solely on the basis of their refusal to accept Islam.

According to Ibn Kathir in his commentary on Chapter 9:5, Abu Bakr al-Siddiq, the first caliph, used this and other verses to validate fighting anyone who either did not pay religious taxes to the Muslims or convert to Islam. Ibn ‘Umar Ibn al-Khattab, one of the hadith transmitters, quoted Muhammad as saying, "I have been commanded to fight the people until they testify that there is no deity worthy of worship except God and that Muhammad is the Messenger of God." He testified that Ad-Dahhak bin Muzahim, an authentic transmitter of hadiths, said that the verse of the sword "abrogated every agreement of peace between the Prophet and any idolater, every treaty, and every term." ‘Awfi cited Ibn ‘Abbas, who argued that "Ultimatum" obviated earlier peace treaties.[60] The Shafi‘i school took this as a justification for killing anyone who abandoned prayer and for fighting anyone who refused to pay increased religious minority taxes.[61]

Such interpretations resonate. Muhammad Sa‘id Ramadan al-Buti, a contemporary Al-Azhar University scholar, wrote that "the verse (9:5) does not leave any room in the mind to conjecture about what is called defensive war. This verse asserts that holy war, which is demanded in Islamic law, is not a defensive war because it could legitimately be an offensive war. That is the apex and most honorable of all holy wars. Its goal is the exaltation of the word of God, the construction of Islamic society, and the establishment of God's kingdom on earth regardless of the means. It is legal to carry on an offensive holy war."[62]

Defensive warfare in Islam is nothing but a phase of the Islamic mission that the Prophet practiced. After that, it was followed by another phase, that is, calling all people to embrace Islam. Even for People of the Book, there can be no role except conversion to Islam or subjugation to Muslim rule. Hence, Muhammad's statement, "They would not invade you, but you invade them."[63]
http://www.jihadwatch.org/2007/09/peace-or-jihad-abrogation-in-islam.html