Lets not kid ourselves though that the people of the middle east had led a peaceful, harmonious life prior to any western aggressions. The long standing Muslim hatred of Jews clearly highlights that the propensity for religious antipathy & violence has always been there
I don't think it's useful to draw a direct link between pre-modern religious attitudes and forms of religious bigotry and violence, and contemporary issues. The experience of being religious in the pre-modern world can't be adequately captured today, it was a time when the existence of God and the assumption that his spirit and will pervaded everything went pretty much unquestioned, bar the odd philosophical free-thinker. The modern world has the effect of calling this and all related assumptions into question, so that to be religious today means in many ways to be
consciously religious. This heightened sense of religious consciousness is akin to being 'born again' or converted, so that sectarian sensitivities move beyond squabbles over who is right or wrong about God to the idea that sectarian rivals are allied to this modernity which constitutes a full-on assault on our very identity.
The problem of Western impact on non-Western societies isn't IMO primarily one of the violence that undoubtedly accompanied it, it's more to do with the uninvited force of this modernity and the subsequent sense of alienation that followed. In terms of the Islamic world, consider this - prior to the 19th c., a Muslim's sense of his place in the world,
as a Muslim, was defined by a range of different beliefs and institutions - belief in God and his final message, belief in the unity (not necessarily political) and primacy on earth of the umma who accepted it, and subsequently the belief in the inevitable triumph of Muslim arms; institutions such as the caliphate, which represented in theory the political unity of the umma, the shari'ah, which ensured a certain measure of legal conformity across a politically divided umma, and the Sufi orders which provided transnational/continental networks for merchants, scholars and travelers to tap in to from Spain to India.
The modernity which arrived with the West undermined pretty much every single one of these - belief in God and his final message by the introduction of Western science; the unity of the umma by the idea of nationalism; the political and military supremacy of the Muslims and the primacy of the caliphate by the triumph of Western arms; the shari'ah by the introduction of Western legal codes; and the Sufi networks by the imposition of modern borders and alternative secular forms of transnational solidarity. So to be consciously Muslim today is in many ways to be confronted with an assault on your sense of place in the world which draws many to the simple and reassuring claims of Islamism in its various forms.
In terms of the Islamic view of the Jews, they were traditionally subjected to the type of pre-modern religious polemic which regarded them as inferior due to the nature of their understanding of God and his will, and this was reflected in the inferior political status accorded them by the shari'ah. Today's Islamist take on the Jews is quite different, it regards them as the ultimate partner or even driver of the modern assault on all that is just and holy in the world, and in this sense is obviously more related to the modern European forms of anti-semitism than to traditions relating to the conflict between Muhammad and some Jewish tribes in the 7th century Hijaz - no surprise since modern Islamist movements owe a lot to the 20th century totalitarians.
This is not to argue that pre-modern Islamic societies were peaceful and harmonious - no pre-modern society was, but the Islamic civilization found a
relatively decent way of regulating sectarian relations so that religious bigotries were rarely expressed with the violence of, say, 16/17th century Europe.