During the Muslim conquests, the point wasn't to "subjugate the indigenous peoples and brutally kill off all that disagreed with them." Actually, it is a testament to their civilized ways that so many actually survived, thrived, and participated in civil society under Muslim rule - there was tolerance for Jews and Christians as well as Zoroastrians and other who were not "of the book." This is in sharp contrast to the bloody mess left in the wake of the crusades - on one of these the crusaders even sacked Constantinople, the city that sponsored them in the first place.