I know its for a closed system, but an omniscient deity can still violate it. Even if we consider that it is outside of the universe, that still composes a closed system. It doesn't matter if he chooses not to, but he still can. An omnipotent being can be considered part of a system that is closed and then violate the second law of thermodynamics. If not, then we have found something that an omnipotent being can't do, which would be contradictory. The only way to reconcile this is to say that the being becomes more disordered, but I'm not sure if that has any meaning for a 'supernatural' being.
You could say that there is a closed system that comprises the omnipotent being and the universe, but what reason would we have to think that the conservation laws apply to that system? The conservation laws are not absolute, there are laws of nature that we've discovered empirically within the context of observations within our own universe. We don't have any good reason to apply those laws to anything outside of the universe.
Sure, we could tag everything we know with "well this doesn't apply in situation X" (here being when the deity acts). I'm sure we would count that as knowledge, right? That would be like saying Newton understood gravity. His laws of motion were accurate, except in situations close to the speed of light. It makes a mockery of what it means to understand something. If something can change around the gravitational constants at will, then that would totally revert our understanding of mass and gravity to square one.
All we are doing is quantifying the law. It's not as if this isn't already done, for instance there is the implicit quantifier,
in the actual world, such that the law is:
In the actual world, the speed of light is the speed limit.
Because surely we don't want to say that's it's logically impossible for something to go faster than the speed of light, just actually impossible. And similarly we can add the quantifier,
for all natural beings. I don't see what the issue is with that.
In any event, it's not at all obvious that the speed of light being the natural speed limit is a necessary law of physics. On the Lorentzian interpretation of relativity, there is no restriction on things going faster than the speed of light, and even on the Minkowskian interpretation, it's not that things can't go faster than the speed of light, it's that particles can't the accelerate from subluminal velocity to superluminal velocity. There is no restriction on particles which always travel at superluminal speeds.
Indeed, Bell's theorem seems to confirm that things can travel at superluminal speeds (from
wiki, "Results of tests of Bell's theorem agree with the predictions of quantum mechanical theory, and demonstrate that some quantum effects appear to travel faster than light."). That's why JS Bell himself advocated the Lorentzian interpretation of relativity ("There is no intention here to make any reservation whatever about the power and precision of Einstein’s approach. But in my opinion there is also something to be said for taking students along the road made by Fitzgerald, Larmor, Lorentz and Poincaré. The longer road sometimes gives more familiarity with the country." -JS Bell,
How to Teach Special Relativity).
Lorentz anticipated the possibility of superluminal velocities and how they would confirm his interpretation in 1913:
"Finally, it should be noted that the daring assertion that one can never observe velocities larger than the velocity of light contains a hypothetical restriction of what is accessible to us, [a restriction] which cannot be accepted without some reservation."
In sum, the speed of light being the "natural speed limit" is not a law of physics but a presumptuous restriction made for the advancement of a Minkowskian interpretation of relativity theory. Anyone who accepts the existence of an omnipotent being is perfectly in line with modern physics to reject that interpretation in favor of a Lorentzian interpretation. Results of Bell's theorem are confirmatory of that position and any new results from CERN would simply be icing on the cake.
By the way, basically everyone in the science community thinks that there was a flaw in that measurement, even the team that recorded it (+1 for skepticism).
And have they succeeded in finding a flaw yet?
If it is an epistemic principle, an omniscient deity would still violate it. You can't say there a principle in which X can't be known, and then say that a being that knows X doesn't violate said principle. The reason we have the Uncertainty Principle is because of the way you get information from (i.e. measure) an object, not because of quantum mechanics.
On the interpretations of quantum physics I'm advocating, the uncertainty principle entails that X can't be known by humans because of the limitations we have in measuring quantum particles, not because of any fundamental indeterminacy of reality itself, hence why the uncertainty is epistemic and not ontic. But for an omniscient being, he wouldn't even need to measure the particles in order to know the facts about position and momentum of those particles. Hence he doesn't encounter any uncertainty problem. So long as propositions about the momentum and position are true, which they are by nature of the uncertainty being merely epistemic, an omniscient being would know them.