First we start with God as the creator.
First you start with God as the creator.
You may wish to assume this, but let's not pretend it's a logical necessity to start with a god/creator being. Imagining that you solve the mystery of where the universe and its complexity came from by simply asserting the existence of yet another complex entity of unknown and unexplainable origins is hardly compelling logic.
In physics nothing breaks the rules. That's why the rules are called rules. If something appears to break the rules, then the problem lies in our understanding of the rules. If you let go of a rock and it doesn't fall to the ground, then either forces other than gravity are acting on the rock, or there's something about gravity we haven't quite grasped yet. One would not generally assume that the rock had made an independent moral decision to disobey the Law of Gravity. Bad rock! Bad, evil, naughty rock!
If we're going to talk about "systems", let's not blur the very important distinction between "law" in the scientific sense and "law" in the moral sense. The former cannot be broken at all, the latter is broken innumerable times on a daily basis -- albeit presumably with negative consequences of some sort. In physics there is no disobedience.
This kind of blurring appears to be going on in other parts of this discussion. Moral relativism is somehow lumped in with "scientism", and consequently the provisional nature of scientific truth is somehow twisted into implying a terribly dangerous "anything goes" moral free-for-all.
The problem with the above is (at least) twofold. The first major problem I see is whether there's any practical basis for concern over the distinction between a religiously derived morality and so-called relativistic morality. Since one is free to choose one's religion, one is free to choose one's own favorite set of "absolutes". Cry all you like about this and that not being "true religion" whenever examples of religious failures are brought forward, if your reason for decrying relativism is that it supposedly opens up the floodgates to moral chaos, it can hardly be said that religion has done a very good job of ensuring morality either.
Hypothetical goodness brought about hypothetical adherence to hypothetical moral absolutes, written up in someone's moral treatise or encyclical, does the world no more good than the imagined hypothetical licentiousness of relativism does the world harm.
At best it might be said that religion turns morality into a "package deal" when you're shopping for a set of moral principles. If one further discounts the amazing human capacity to rationalize any set of rules into an excuse to do as we please, one might claim that moral package deals perhaps keep the citizens more in line than the "a la carte" morality that relativism supposedly leads to -- even then, that's just hypothetical, it's hardly proven.
The second major problem I see here is confusing the quest for truth with the quest for values. Consider these assertions:
A) The Earth orbits the Sun at an average distance from the Sun of approximately 150,000,000 kilometers.
B) Murder is wrong.
Assertion A is very clear in meaning. The truth of the assertion can be tested by many means and matched against plenty of available data.
Assertion B is not at all clear. Even though murder is widely taken to be wrong across many culture, faiths, philosophies, and personal beliefs, the meaning of "murder is wrong" is still not clear, because "murder" and "wrong" are not concrete words. What one calls murder, another calls a justifiable execution. What one calls murder, another calls "unavoidable collateral damage". We could go on and on about what "wrong" means to different people.
I think the scientific mind can be applied to moral questions. It can be used to seek logic and consistency, it can be used to evaluate the real-world consequences of moral decisions, to clarify causes and effects, to distinguish causation from correlation. But just as mathematics relies on fundamental postulates, morality relies on fundamental values, and those values cannot be discovered as if they're "out there" to be found, they cannot be deduced, they cannot be proven or disproven.
Any statement of moral truth must ultimately be rooted in fundamental values which one simply either accepts or does not accept. I see no way to escape the personal, individual element in this. If you say "murder is wrong", I can always say "So what?" I can even believe you're right that murder is wrong, but simply not care about being right or wrong. I have to choose to value the lives of others. I have to choose to adhere to a moral vision and to care about how well I adhere to it.
Religion offers no way out of this ultimately personal element of morality and ethics. All it does it offer unproven incentives and disincentives in an effort to persuade one to care about one's moral choices based on these asserted consequences... like offering up Eternal Salvation as a reward and Eternal Suffering as a punishment for not "getting with the program". As humans are free to chose among many religions (and even invent new ones whenever it suits them) there's not one reason to suppose that religion offers any way at all out of the open-ended nature of values choices, nor any reason to believe religion offers any magical, mystical access to those things the human mind can't find certain answers for on its own.