Well, actually, i'm gonna say this to ya...
Well, when first playing the game ( i dunno know if you r a muslim or not, so..) and reaching that level, I've heard the chanting right away. I thought about it, and it can be looked at it in 2 ways:
one way, the thing i said earlier,
2nd way: Well, nonbelievers went to hell, now pray to god to let them to heaven.
For the shield, basically, yea, what you said is true.. but still, if it wasn't any evil to muslims, then shigero miamoto wouldn't change it, would he? Well, maybe he thought it was wrong to use religious aspects in a game, so he removed it..