Actually, you've taken his "ordered universe" statement way out of context.
Sounds to me like you're blaming God for something he doesn't have a direct hand in. And that commandment, btw, is 'thou shalt not murder, which implies two things - the one being killed is human, and is being killed for no justifiable reason.
No. Like I said, it's balanced. All creatures do have an opportunity for life, because each one has both it's own defense mechanisms and its own particular method of acquiring food, be it agility in hunting, waiting in ambush, or setting 'traps.' Or whatever.
If you have a reason, it's no longer an assumption.
No. 'Morality' exists for a related reason though, which I'll get to in a moment.
I like these two definitions of a spirit:
1. The vital principle or animating force within living beings.
2. Incorporeal consciousness.
The spiritual would be anything relating to these things, in addition to, for example, beings which exists only (or at least originally) in a non-embodied form. Simply a matter of existing differently than us.
The reason for morals (in Christianity anyway) that seem to be in excess of the Golden Rule is because they are believed to cause damage to one's spirit, but not necessarily to one's flesh. Being that the spirit cannot be seen with a natural eye, we tend to determine morals based only on what we see. If more is being done to our spirit, it would be incredibly unfair for a God who can see such things (being a spirit and all) to not inform us of it.
Spiritual vs. physical is not to dissimilar from a theory of parallel universes/dimensions. Matter in our universe is adapted to certain laws of physics. If in another universe physics were completely different, it stands to reason that matter (if it could still be called that) and life would adapt to it differently to abide by those laws, laws which we, not living in that nature, wouldn't have a good chance of understanding. At all.
The difference is that the spiritual and physical are supposedly interconnected. Much in the way that 2D is connected to 3D, but at a higher level. I'll use that analogy to attempt to illustrate what I'm saying. Let's say we have a 2D person (I know, 2D people don't actually exist, except perhaps for Kate Moss), and we have some sort of square box in front him. We, in 3D, could see inside the box, the 2D person could not. If the person were to go inside the box, we could still see him with no effort, the 2D person could not see us because that field of vision simply doesn't exist to him. If we were to do something ordinary in 2D, it would be deemed a "miracle" by the 2D guy.
Apply that to the physical and spiritual, and you have the same scenario. The spiritual "dimension" would reside above the physical, be linked to it, yet we could not see anything in it unless it first interacted with us, or unless we had a spiritual element of our own. This would explain why it seems that in the Old Testament, God doesn't seem to regard physical life too much. And why would he concern himself with only the temporary part of our existence?
In this way, God could be right next to you and you wouldn't even know it.
So hopefully, I didn't suck too much at explaining that viewpoint. :-\