Well first I don't think a computer (at least a deterministic one) will ever be powerful enough to "perfectly simulate the workings of the human brain". That would be a quantum N-body simulation with N > 10^23. There probably isn't enough matter/energy in the universe to do that.
When people talk of simulating the human brain they mean something along the lines of : if we assume that the function of the human brain is entirely determined by the transmission of electrophysiological signals between neurons then we will be able to simulate that behavior in the not too distant future.
Personally I think we'll have general AI's, machines which can pass the Turing test, well before such simulations have been developed.
In either case I can't see how a CPU could become sentient just because of the software it's running. Think about it. Do you worry that you're CPU might be suffering when you drive it hard ? If the simple fact of running the right software can allow a piece of silicon to feel pain then that's something that my model of physical reality can't account for.
Do you worry that you've died and a new, unrelated consciousness born every time a cosmic ray pops a single electron in your brain up to a higher orbit? It seems obvious from the amount of mechanical or chemical intervention that's required to create a detectable change in consciousness that the human substrate for consciousness only matters at a far more macroscopic level than the quantum.
Also, I think that the amount of worry you experience over whether a computational substrate running software designed without consciousness in mind can suffer is a very, very, very poor proxy for the question of whether machine sentience is possible. Think about it. If you did have a magical hypercomputer, and a program running on it which ran a perfect quantum simulation of a human baby in unbearable pain, would you remain completely blasé?
A superconductor doesn't stop being a superconductor if a cosmic ray ejects one of its electrons. It would however be erroneous to conclude from that fact that quantum mechanics plays no role in superconductivity.
I don't think your true objection is based on quantum mechanics. Based especially on one comment[1], I think you're making a hidden assertion that subjective experiences carry moral weight only if they cannot be explained in terms of other understood phenomena.
I'd like to examine this assertion: If someone could prove to your satisfaction that your present conscious substrate is something other than a human brain--say, a computer program with inputs provided by an advanced android body in the real world--would you consent to undergo the proverbial 50 years of torture in exchange for a dollar donated to your favorite charity?
Well obviously everything is based on quantum effects. When a transistor changes its state, quantum effects need to happen. But I don't think it's legitimate to postulate that the whole complexity of the quantum state is necessary to simulate the behaviour of a transistor.
I also think that general AIs will not be the kind that simulates brains.
But I think its wrong to tie consciousness to the hardware its running on. Consciousness is a property of the software. I think its fallacious to postulate a difference between an intelligence that runs on brains and an intelligence that runs on other machines if the difference can't be observed.
And yes I would be worried that a robot might suffer if it is sufficiently advanced to exhibit the same behaviour as, say, a cat.
What if the computer were powerful enough to perfectly simulate the workings of a human brain? Does that brain not have a consciousness?
[1] http://en.wikipedia.org/wiki/P-Zombie