What Sam Harris is saying, I think, is that religion was our explanatory model for things that happened which we could not understand. But as we evolved, gained more experience and knowledge, and built sophisticated tools, science became our go-to frame of reference. To say that religion, now or then, is indicative of science failing to explain something is curious, however. Scientific failure is a plausible enough way of putting it, but I prefer to acknowledge that science can carry us quite far, but only so far, beyond which other viable explanatory models must come it (rf. The Tripartite Model). So science doesn't so much fail, as it meets its limits with certain phenomena and in certain contexts.
Harris' point about the wide diversity of religious belief, practice and terminology is a good caution not to pin religion down as meaning one, and only one, thing. But he must be very careful not to suggest that Islam, in particular, is a religion of Holy Wars and of combat and death in certain contexts, which is the highest obligation for Muslims. Islamic scholars and Muslim practitioners can speak to this much better than I can, but Islam is a religion of peace. But like Christianity, people can commandeer the religion to justify a destructive or military purpose (rf. English kings who fought wars in the name of God).
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