The Koran says...
"And kill them wherever you find them, and drive them out from whence they drove you out, and persecution is severer than slaughter, and do not fight with them at the Sacred Mosque until they fight with you in it, but if they do fight you, then slay them; such is the recompense of the unbelievers" - ( 2.191).
but it also says...
"You shall have your religion and I shall have my religion" - (109.6).
So what do we make of that? I'm not convinced that the Koran is an uncomplicated manifesto for bloody religious uprising. I suspect its as contradictory as many other holy books can appear to those who don't believe in them.
Books that are contradictory but inspire religious devotion can be picked and chosen from - interpreted - and I think that goes some way to explaining the radically different behaviours of the Janjaweed and some of the Muslims I know.
I guess this won't satisfy you - and a mention of the old testament verses that sound a bit queazy - like say Numbers 31:1-54, which seem to indorse massacre and rape on ethnic or religious grounds, won't seem relevant.
The fact of the matter is that I have difficulty trying to differenciate between Christian and Islamic calls to arms like this and would be very interested if you could explain how they differ.