Janissaries were slaves kidnapped, bought or received as a tithe mostly from Christian communities.
But they were all of course islamized and properly indoctrinated at an early age.
That said, unlike Christianity medieval Islam was often quite tolerant and enlightened, Ottomans being a great example here. Folks here seem to base their perception of medieval religious strife off of Christianity, but that's just one religion. And even medieval Christians had times when they were not irredeemably evil bustards. Like Spain during early Reconquista.
