Mr_Bovinity,
It is obvious you have given this issue much thought and your response appears to be sincere; but unfortunately, ill-founded. While I would like to respond in detail my energy is limited by my present circumstances and I reserve what I have in my appeals to a broader audience. However, I will respond on three key points.
First, you imply historical equivalence to the actions of Christians (the Crusades) which occurred over 800 years ago to modern radical, Islamist Jihad which began in the 20th century and continues to this day. The wide historical gap between how today's actions of murderous Jihadists can be justified by actions that occurred over 800 years ago begs credulity.
Second, you imply moral equivalence between a religion that seeks to define the relationship between God and man, and between men, based on peace, love and forgiveness to that based on submission to an uncaring, unknowable God who demands the destruction or subjugation of all those that don't believe. One represents free will (Christianity) while the other offers forgiveness for faith in a fatalistic excuse for the inability to choose between good and evil since all is preordained and known (Islam). This moral relativity is a symptom of the disease that defines our present dilemma.
Finally, you allude to a supposed 'Golden Age' of Islam defined by tolerance. It is a myth. The mythical golden age, that of Granada, was defined by intermittent periods of relaxed dhimmitude punctuated by terror as exemplified by the one day massacre of over 5000 Jews and the expulsion of the rest from present day Spain by the Muslim occupiers. In fact, the Inquisition you mention was modeled on its Islamic predecessor.
Again, your arguments are appreciated, appear sincere and are hopefully based on some study of the issues. If you would like to pursue other sources of information on the topic I recommend you check out my profile for a growing list of bibliographical sources. I do not come to this debate unarmed and totally ignorant and I assume you do not either.