I think I said it in an earlier thread already, but for now I will believe the chakra indeed comes from the sacrifice - but with a twist. I reckon burning the soul and body like that might allow the zombie to use far more chakra than a living human could pump out of his system in a limited time. Naturally it annihilates the victim in the process. Think of it like using a lifetime's worth of chakra in a moment.

Completely destroying the zombie should be very detrimental since these guys have that control kunai embedded into them. One would think removing it (or removing the body from around it) would equal to removing a system disk from a computer... So, I think the question of what would happen with the spirit/body in that case is not relevant.